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.