Row 1: Finder, Path Finder, Dashboard, Controller Mate, Script Editor, Time Machine, Spaces, Console
Row 2: Activity Monitor, Sys Prefs, iCal, Addr Book, OpenOffice, Firefox (Vista), IE (Vista), Chrome (Vista)
Row 3: Firefox (Mac), Safari, Pages, Numbers, Keynote, Zterm, Fusion, VI Client (Win 2003)
Row 4: Xen Center (Win 2003), Terminal, X11, Mock-ups, Flex Builder, Eclipse, Xcode, IB
Row 5: iPhone Simulator, Instruments, BBedit, RoaringDiff, DoubleTake, Graffle, Photoshop, Dreamweaver
Row 6: FinalCut Express, iTunes, iChat, iPhoto, Dictionary, Preview, ScreenSharing, VMware Infrastructure Update
The Windows icons are split between Vista and 2003 VMs.
The big app that I use that's not listed is Things, which I run on my laptop.