These are links to some of our favorite windows applications organized by category. All of these applications are legitimate programs so you shouldn't have to worry about them containing viruses or malware.

Anti-Virus / Anti-Malware

ComboFix -- Anti-Malware scanner and removal tool.
MalwareBytes -- Anti-Malware. Just download and use the free version, then uninstall after your computer checks out clean.
SUPERAntiSpyware -- Spyware detection and removal tool.
SpyBot Search and Destroy -- Spyware detection and removal tool.
AVG Anti-Virus Free Edition -- Excellent anti-virus protection. Lately they have been more agressive in trying to get people to upgrade to the paid version through some annoying pop-ups that happen every couple weeks or so.
Microsoft Security Essentials -- Antivirus and Anti-Malware protection. Works great with Windows 7.

Email Clients

Thunderbird Email Client -- More stable than Microsoft Outlook.
Google Galendar Tab -- Add on for Thunderbird to put your Google Calendar in a Tab
Outlook Dedupe Tool -- A free tool for when Outlook breaks your inbox with 200+ duplicate messages.

Web Browsers

Firefox -- The best web browser available. It's always good to have a backup web browser in case Internet Explorer breaks.
Reminder Fox -- A calender and todo organizer add-on for Firefox.

PDF Utilities

BullZip PDF Printer -- Turn any document into a PDF just by printing.
CutePDF Writer -- Create PDFs without watermarks.
PDF-XChange Viewer -- Not only a viewer but and editior as well!
Nitro PDF -- Create PDF Files, Comment and review, make PDF forms.

Virtualization

VirtualBox -- Run Windows, Linux, Macintosh and OpenSolaris virtual machines. Binaries are available for Windows.
Synergy -- Use one keyboard on multiple systems without the need of special hardware.

Android

Root Your Droid -- An always up-to-date guide on rooting your Android phone.

Misc

Soluto -- If a virus/malware isn't making your machine slow, this utility may help you figure out what process *is* making your machine bog down.
Ninite -- Silent unattended installation builder with many options. Saves tons of time setting up multiple computers.
Windows SteadyState 2.5 -- Lock down user accounts in Internet cafes, libraries, etc.