I would love to get feedback if I'm missing a really great program that would enhance my quality of life and make me wonder how I ever lived without it.

Network and Internet

Web Browser

Email and News

• Thunderbird: Excellent email and news client. (Although honestly, since switching to Gmail, I don't really use Thunderbird much anymore.)  Even if you only use Gmail, Thunderbird is still useful for offline backups.

Remote Desktop Access

• UltraVNC: Remote desktop control.  TightVNC is my second choice, but Ultra is a bit more polished and has encryption plugins.

Remote Shell Access

• PuTTY: Awesome ssh/telnet/rlogin client.  There is nothing else even close.

Graphical File Transfer

• Filezilla: Great ftp/sftp client; can handle sftp over ssh2 and other variations. 
  
• Another good client is WinSCP, but Filezilla still wins, IMHO.

Chat and Instant Messaging

• Pidgin: Chat client for AIM, IRC, MSN, ICQ, Yahoo, Jabber, etc. (Formally known as GAIM.)   You can also get a Facebook chat plugin. 
  
• Google Talk: If voice chat is important to you, the near-perfect sound quality of Google Talk pushes it to the front of the pack.
• Skype: Need group voice chat or even video chat?  Skype is the way to go.
  

BitTorrent

• uTorrent: Lightweight, yet powerful, BitTorrent client.

Servers

• XAMPP: Apache web server with add-ons like MySQL, PHP, Perl, FileZilla, etc. (Don't forget to secure the installation before using on networked PC!)

Tools

• Wireshark: Network protocol analyzer.  For those of you keeping track, this used to be called Ethereal.

Note: I don't list a firewall anymore because A) since Windows XP SP2, the built-in firewall is half-way decent and B) a hardware firewall on a NAT router is by far the better choice anyway.

Document and Text

PDF Viewing

• Adobe Reader: The original and best PDF viewer. Unfortunately, it is the most bloated as well.
• A great alternative is Foxit Reader. It opens unbelievably fast compared to Adobe Reader, and it works from a flash drive since there is no install. For me, Adobe Reader still wins because of its superior searching capabilities.

PDF Creation

• PDFCreator: PDF print driver, turns any application into a PDF writer

eBook

• calibre: All-in-one ebook manager.  Whatever you need to do to/with an ebook, this will do it.  I use it to convert various formats (including PDF) for use with Stanza on my iPhone.  Completely replaces the Stanza desktop client, and does a better job converting the files.
  

TeX/LaTeX

• MiKTeX: A port of the LaTeX document publishing system. Output can be PDF, HTML, etc.
• TeXnicCenter: LaTeX IDE, including editor, spell checker, symbol toolbars, etc.
• Texmaker is a decent alternative because it is more portable than TeXnicCenter, but I still prefer TC.
  

Office

• OpenOffice.org: Word processor, spreadsheet, database, and presentation applications. For nearly all intents and purposes, this is a total (free) replacement for MS Office.

Text Editing

• Vim: Powerful keyboard-based text editor, steep learning curve. Not for everybody. 
• Notepad++: My text editor of choice for everyday editing and programming. The main limitation is that it can't handle big files very well (say ~100MB), and it won't open really big files (say ~250MB) at all.
• WriteMonkey: Full-screen, distraction-free text editing seems to be all the rage, and WriteMonkey fits that bill nicely.  These types of apps don't usually have a ton of features, as they focus on reducing on-screen clutter more than anything else.  But having said that, WriteMonkey has also been adding quite a few neat features lately and I think it leads the pack in functionality.
  
• If you like this sort of thing, you might also want to check out Q10, Dark Room, or jDarkRoom.
• Honorable Mentions:
• PSPad: Feature-rich programmers text editor with console output and code explorer windows. Maybe a tad heavy for plain old text editing.
• ConTEXT: Less full-blown than PSPad, maybe more suitable for editing simple text.  Makes a good Notepad replacement, but Notepad++ is still better IMHO.  Regular expression searching is good.

Mathematics

Calculator

• SpeedCrunch: Calculator with FAST start-up and plenty of functionality.  This is the first app I reach for when I need to do some simple math.
• Calculator.NET: If you really like to use RPN notation (similar to historic HP calcs), this is a nice, simple calculator.  Its slow start-up has always annoyed me though.
  

Symbolic Computation

• Maxima: Full symbolic computer algebra system.  Comes with wxMaxima, which is an easy-to-use graphical interface.

Numeric Computation

• Scilab: Numerical computation program, similar to Matlab in functionality.

Programming

Version Control

• Subversion: Command-line version control system with repository server. 
• TortoiseSVN: Excellent graphical Subversion client.
• Bazaar: A distributed version control system.  This is nice for personal use because you don't need to run a server.  For remote usage, an ssh tunnel works well.

Installer

• Inno Setup: A great installer for packaging your own software

Scripting Language

• Python: A great general purpose programming language

Additional Python Packages

• wxPython: My favorite cross-platform GUI toolkit.
• PyGTK: Another GUI toolkit that rivals wxPython in many respects.  I still prefer wxPython because it uses native widgets when it can.
• Pmw: A GUI toolkit extension used on top of Tk. There is little reason to use this anymore since wxPython and PyGTK are far better (although probably more bloated) that the Tk solution.
• Reportlab: PDF generator
• NumPy: math module (replaces Numeric and Numarray)
• py2exe: Creates "exe" files
• SciPy: Scientific package useful for everything from plotting to linear algebra.
• PyCrypto: Cryptography package
• PyEnchant: Spell-checking package
• Matplotlib: 2D plotting library
  

Utilities

Compression

• 7-Zip: archiver with great compression, useful from command line, nice GUI and Explorer integration, and it is fast.
• PeaZip: If 7-zip doesn't work for you, PeaZip is the place to look.  It supports basically every format you will ever encounter.
  

Encryption

• TrueCrypt: on-the-fly disk and file encryption. Works absolutely seamlessly with the OS so you wouldn't even know you are using an encrypted disk.
• GPG: GNU Privacy Guard for cross-platform file encryption/signing.
• I don't like listing programs with duplicate functionality, but each of these programs has its uses, and I haven't decided which to use exclusively yet. They both rely on GPG (and require it to be installed independently), so files encrypted in one can be decrypted by the other.
• GPGee: Nice and simple shell integration and front-end for GPG.
• WinPT: Another front end for GPG with more features than GPGee. Can be used where shell integration isn't an option (like where you can't install software.)

File Deletion/Recovery

• Eraser: Secure deletion with a nice GUI and Explorer integration.
• CyberShredder is a good alternative for USB drives when you can't install a shell extension.
• SDelete: Also good for USB drive, this is a command-line secure delete that wipes free-space too.
• Between these two programs, you should be able to recover any file that is physically possible to recover without special hardware:
• Recuva
• Zero Assumption Recovery (the free version gets the job done)
  

Anti-Virus

• AVG Free Edition: Nice anti-virus program with frequent virus definition updates. As a bonus, it is very light on system resources. (Not licensed for commercial use.)

Process Management

• Process Explorer: List and interact with processes and file handles.

File Management

• WildRename: Wonderfully full-featured file renaming utility that supports regular expressions.
• WildReplace: Search for files and replace text in the files.
• Filemon: Monitors file access in real time. Useful for identifying i/o hogs.

Command Line

• Console: A terminal app that is better looking and more configurable than cmd.exe (although it is just a wrapper for cmd.exe).
• UnxUtils: Unix-like command-line tools compiled natively for Windows (i.e. no cygwin dependencies).
• PsTools: Command line tools for managing processes, services, and remote administration. psexec is especially useful to issue a remote command.
• Blat: command line email, useful for automated backups to remote servers.

Launchers/Shortcuts

• Executor: Command-line launcher that is highly customizable.  Similar to Launchy, but I like Executor better.
• Pstart: Customizable menu-based launcher.  I never use the "Start" menu anymore.  It takes to long to find stuff.  I have Pstart configured to pop up by right-clicking on the right side of the screen. 
  
• AutoHotKey: Just like it sounds... automate stuff with hotkeys.
  

Backup/Synchronization

• SyncBack Freeware: Backup and synchronization program. Make sure to get "SyncBack Freeware" since the other product, SyncBackSE, is not freeware.

Password Management

• KeePass: Truly excellent password manager that is capable of running from a USB flash drive.

Other

• Unlocker: Windows XP has a terrible habit of locking folders that are empty so you can't delete them until you reboot. This program frees up these folders for deletion. Simple right-click interface.
• TaskSwitchXP: This is the task switcher that Windows should have shipped. Nice eye-candy too.
• E-Sword: Bible software with multiple translations and study aids.
• Virtual CD-ROM Control Panel: Unsupported tool from Microsoft that mounts disk images (iso files) as a virtual cdrom drive.
• Virtual Dimension: Virtual desktop switcher with some advanced features. It has good hotkey support and allows you to assign (or reassign) windows to a particular virtual desktop or all of them. (The Virtual Desktop Manager Microsoft PowerToy doesn't have that last feature, which makes it nearly unusable.)

Microsoft Powertoys

• All of the Microsoft Powertoys can be found here. These are the ones I occasionally use:
  • Powertoy Calculator
  • Resize Powertoy
  • Tweak UI
  • ClearType Tuner

Multimedia

Media Players

• VLC: Video player for nearly any format imaginable. Especially useful for playing videos with obscure codecs, e.g. a clip encoded in some strange AVI variation.
• iTunes: Audio and video player that makes keeping your music organized easy.  A must-have for iPod users.  (Well, not "must"; there are alternatives, but iTunes is great.)
  
• XMPlay: If you need something portable, lightweight, and fast, this skinable audio player is a great alternative.  It supports nearly every useful audio format and has great global hotkey support. Lacks a good playlist editor though.  I only use this from portable USB drives, otherwise I use iTunes.

Audio Ripping/Encoding

• CDex: Rip and encode CDs to Ogg Vorbis, MP3, etc. with automatic naming thanks to freedb support.
  

Media Conversion

• MediaCoder: Convert from/to nearly any video and audio format, including extracting audio from video.
  

Audio Editing

• Audacity: Full-featured multitrack audio editor.

CD/DVD Burning

• ImgBurn: Lightweight CD/DVD/HDDVD/Blu-ray burning application that does everything I could possibly want to do.  No need for anything else.
  

DVD Ripping

MP3/OGG Tag Editing

• Mp3tag: Unfortunately named universal tag editor that works with lots of formats other than mp3. Supports regular expressions, online freedb database lookups, playlist creation, etc.

Video Editing

• VirtualDub: Video capture and editor. Not a whole lot of open source options in this field, but this gets the job done.

3D Rendering and Animation

• Blender: 3D modeling and animation. Has more power than I have skill, but other people do really cool things with it.

Image Viewing/Editing/Browsing

• Picasa: While pros would sneer at it, this is by far the best application for normal people to prepare digital photos before sending them out for developing. Its slick interface makes tasks like cropping (to a standard size!) and color correction simple. Seems a bit heavy on PC resources, but it is plenty fast on any newer computer.
• GIMP: Powerful image/photo editor like Photoshop.  Not necessarily appropriate for a casual user who just wants to crop some photos. The scripting allows for complex plugins and automation.
• A good alternative to GIMP for those weary of the learning curve (or the name) is Paint.NET. It is like a beefed-up version of MS Paint.  It is really polished, but I generally use GIMP instead.

Screen Capture

• WinSnap: Bind this screen capture program to the PrintScreen key, and you'll never look back. Nice feature set that includes fancy handling of rounded corners and transparency. Free for non-commercial use.
• Gadwin PrintScreen: Alternative to WinSnap if the non-commercial license is a problem.

Vector Drawing

• Inkscape: Creates vector based images like diagrams and logos.

Comic Reader

Fonts

Unicode Greek

• Galilee: A wonderfully legible font appropriate for typesetting ancient Greek.

Microsoft ClearType Font Collection

• Microsoft bought some truly great fonts to include with Vista.  These include Calibri, Candara, Consolas, Cambria, Constantia, and Corbel.  If you don't have Vista or MS Office 2007, you can get them by installing either the free Powerpoint 2007 Viewer or the Microsoft Office Compatibility Pack.

Monospace

• Consolas: Awesome TrueType programming font designed by Lucas de Groot to work with ClearType, so be sure that ClearType is enabled.  This is part of the Microsoft Cleartype Font Collection, so you don't need to download this installer if you already have the collection.
  
• Dina: Great bitmap font in 8, 9, and 10 points with normal, bold, italic, and bold/italic faces. This is a wonderful font for programming, consoles, and PuTTY. I like the 8 and 10 especially well; the 9 is a bit tall for the width. Dina is so clear and crisp that it is actually pleasurable to read. I'm looking at it right now and it makes me happy. Looks great on LCDs or CRTs.