While the categories for the Portable Apps seem pretty logical, I see a lot of programs fall in the "Other" category for Utilities. (about 10!)
I also noticed that some of the categories didn't quite fit.
While it may seem like a lot to modify all of the existing apps to fit this category, it probably could just be implemented in new apps and app updates. Here's a little more of what I figured might have made more sense:
Accessibility
> On-Screen Keyboards
>> On-Screen Keyboard Portable
> Screen Magnifiers
>> Virtual Magnifying Glass Portable
Audio & Video
> Audio Editors & Converters
>> Audacity Portable
>> BonkEnc Portable
> Disc Burning & Authoring
>> DVDStyler Portable
>> InfraRecorder Portable
> Media Players
>> CoolPlayer+ Portable
>> MPlayer Portable
>> VLC Media Player Portable
> Video Editors
>> VirtualDub Portable
Development
> Packaging Tools
>> NSIS Portable
> Web Development
>> Nvu Portable & KompoZer Portable
>> XAMPP
Education
> Religion
>> BPBible Portable
> Science (even though the only ones we have are astronomy, it seems logical to make this a science category for future apps)
>> Celestia Portable
>> Stellarium Portable
Games
> Adventure Games
>> The Mana World Portable
> Arcade Games
>> LBreakout2 Portable
> Board/Card Games (these two seem to pair up, even if there's only one card game)
>> PokerTH Portable
> Emulators
>> DOSBox Portable
> Other Games (I don't think there will be many, if any other music games)
>> Frets on Fire Portable
> Puzzle Games
>> Jooleem Portable
> Strategy Games (Minesweeper and Sudoku fit in this category better than puzzle games)
>> Mines-Perfect Portable
>> Sudoku Portable
Graphics
> 3D Modeling & Rendering
>> Blender Portablehttps://portableapps.com/node/add/forum/5
> Image Editors
>> GIMP Portable
> Image Viewers & Managers
>> Cornice Portable
Internet
> Web Browsers
>> Mozilla Firefox, Portable Edition
> Instant Messengers
>> aMSN Portable
>> Miranda IM Portable
>> Pidgin Portable
> Download Managers & Accelerators
>> WinWGet Portable
> Email Clients
>> Mozilla Thunderbird, Portable Edition
> FTP, SFTP, & SCP Clients
>> FileZilla Portable
>> WinSCP Portable
> Telnet & SSH
>> PuTTY Portable
Office
> Document Viewers
>> Sumatra PDF Portable
> Calculating Tools
>> GnuCash Portable
>> SpeedCrunch Portable
> Organization
>> Mozilla Sunbird, Portable Edition
>> PNotes Portable (I don't know where to put this)
>> Task Coach Portable
> PDF Editors
>> PDFTK Builder Portable
> Suites
>> OpenOffice.org Portable
> Word Processors
>> AbiWord Portable
Operating Systems
> Macintosh
>> Mac-on-Stick
> Linux
>> "Coming Soon"
Utilities
> File Compression & Archiving
>> 7-Zip Portable
>> PeaZip Portable
> File Managers
>> Xenon File Manager Portable
> Other
>> ConvertAll Portable
>> Java Portable
>> Java Portable Launcher
>> Lightscreen Portable
>> WinMd5Sum Portable
> Security
>> ClamWin Portable
>> Eraser Portable
>> KeePass Password Safe Portable
> Synchronization
>> Toucan
> System
>> Command Prompt Portable
>> JkDefrag Portable
>> WinDirStat Portable
> Text Editors
>> Notepad++ Portable
>> WinMerge Portable
PortableApps.com
> PortableApps.com AppCompactor
> PortableApps.com Installer
> PortableApps.com Platform (this should have its own page, not just a link to the suite page)
> PortableApps.com Suite
App Extensions
> BonkEnc Portable
>> LAME MP3 Encoder
> GIMP Portable
>> GIMP Portable Background Window
>> GIMP Portable Help
>> GIMP Portable Photoshop Layout
> Mozilla Firefox, Portable Edition
>> Accessibility Extension
>> DownThemAll! Download Manager Extension
>> FireFTP FTP Client Extension
>> Sage RSS Extension
> Mozilla Thunderbird, Portable Edition
>> Lightning Organizing Extension
While it does seem like a low-priority, not-worth-it idea, I figured I would mention this anyways. And yes, I guess I'm being far too picky on this, but still, I think it would be a good idea to do this, even if it is just for newer apps.
While the categories may need some reorg-ing, a lot of your sub-categories have only one or two apps each in them.
This will overly complicate the process of browsing for apps.
My suggestion for "extensions" is to list them directly below the app that they are associated with -
Or, put them on the DL page for the main app (like is currently done with the GIMP). But give them buttons instead of links to make them stand out.
I made this half-pony, half-monkey monster to please you.