This post has kindly been continued below 
Please note, I do not add ALL new apps etc, some dev stuff and things like themes are not added to keep this from getting cluttered.

PC/MAC Apps
iPhone Tunnel Suite (PC) Lets you tether your phone and file browser WebsiteiPhone PC Suite (PC) Range of different functions Website
DiskAid (PC and MAC) File Browser Website
Media Monkey (PC) iTunes replacement (support for 2.0 is coming) Website
iBaReS (Mac) Backup and restore solution Website

Installer 4.0 
Still in beta.

Installer Repositories
A27 Dev Team: http://a27dev.com/installer/repo
BigBoss:http://apptapp.thebigboss.org/repofiles/installer4/
GPDA: http://gpda.ru/r (Tweaks)
Hackint0sh: http://hackint0sh.org/repo/ (Hackint0sh official)
Handheld: http://i2.handheld.com.vn/ (Community sources)
iClarified: http://installer.iClarified.com (Repo Sources)
iFon Norway: i.iFon1.no
iSpazio: http://repo.neolinus.org/ispazio/
Modmyifone: i.modmyi.com (Community sources)
Navco: http://www.navco786.com/repo (UK Edge Settings)
RiP Dev: http://i.ripdev.com
Sendowski: http://sendowski.de/iphone/
Ste: http://repo.smxy.org/installer4/


Cydia 
Released, growing app support daily.

Cydia Repositories
BigBoss : http://apt.bigboss.us.com/repofiles/cydia/
Free Coder: http://iphone.freecoder.org/apt/
Hack&Dev.org: http://iphone.hackndev.org/apt/
iFonetec: http://app.ifonetec.com/cydia/
Intelliborn: http://intelliborn.com/cydia/
iPhone Video Recorder http://www.iphonevideorecorder.com
iSpazio: http://ispaziorepo.com/cydia/apt/
ModMyiFone: http://modmyifone.com/repo/
SaladSoft: http://nickplee.com/cydiasource/
Ste: http://repo.smxy.org/cydia/apt/
Steffwiz: http://steffwiz.webs.com/iPhone/Repo
Telesphoreo Tangelo: http://apt.saurik.com/
Urban Fanatics: http://urbanfanatics.com/cydia/
Weiphone Source http://app.weiphone.com/cydia/
ZodTTD: http://www.zodttd.com/repo/cydia/

Working Apps 
- 2.0 Safari Patch (cydia) Adds file:// support in Safari for viewing files offline
- AppBackup (cydia) Backup and restore App Store Apps Website
- AppFlow (cydia) An application launcher using coverflow Website
- AirHockey (cydia) An airhockey game Website
- BiteSMS (Installer) Send cheaper SMS’s Website
- Book Reader (cydia) HTML Book reader
- BootNeuter (cydia) Official unlocker for 2.0 Website
- Boss Tool (cydia) Moves hardisk space around
- BossPrefs Safari DownLoad Control (cydia) 
- BossPrefs (cydia) Number of settings tweaks Website
- CallME (installer/cydia) Tapdial clone
- Catagories (cydia) Sort your apps into sub folders Website
- Customize (cydia) customizes the look and feel of the phone Website
- Cycorder (cydia) free iphone video recorder 
- dict (cydia) Client for accessing online dictionaries
- Dock (cydia) quick app switching Website
- Erica Utilities (cydia) A collection of command line utilities Website
- Enhanced CTorrent (cydia) A bittorrent command line client Website
- FileViewer (cydia+Installer) Reads local files like PDF, HTML and images
- Flixwagon (Installer) Broadcast to flixwagon.com Website
- gpSPhone (cydia) Game Boy Advance Emulator Website
- GRIS (Google Reader iPhone Sync) (cydia) RSS client for google reader
- gTxtEdit (cydia/Installer) A text editor for 2.0 Website
- iBlacklist (cydia) filter incoming/outgoing calls/SMS Website
- iCaller BR (cydia) Clear individual calls from your history
- iCommander (cydia) Small file manager Website
- Insomnia (cydia/installer) Allows applications to continue running in sleep mode 
- Intelliscreen (cydia) Calendar, Mail, SMS, News Sports and weather on Lock Screen Website
- iPhone Video Recorder (cydia) remember to add the repository, Cycorder is free Website
- iReboot (cydia) Easily reboot and respring your iphone Website
- iTextUploader (cydia) store your SMS’s at youarchive.it Website
- Kate (Installer) A collection of tools and toys for iphone
- Keyboard Autocorrect disable (Installer)
- Lighttpd (cydia) Website
- Lockdown (cydia/Installer) Password protect applications
- Macman (cydia) A pacman clone
- Make It Mine (MIM) (cydia) Change your carrier name
- Metronome (cydia) 
- MiVTones (cydia) Video ringtones
- MobileTerminal (cydia) a command line terminal Website
- ModPlayer (Installer) Mod player that supports a huge variety of formats
- MxTube (cydia) download youtube videos
- NemusSync (Installer) sync iPhone calendar with Google calendar Website 
- NES (cydia) NES emulator
- openSSH (cydia) Website
- OfflineMaps (cydia) Use a pre-downloaded map in Maps.app Website
- PhoneZap (Cydia) Send geo-tagged pictures Website
- Poof (cydia) Hide icons
- Power Tool (Installer) Enable verbose boot, power down, reboot etc
- Pysl (cydia) call and sms filtering Website
- Qik (Installer) Live video streaming to the web Website
- Quake4iPhone (cydia) Quake…. For iphone Website
- Rename (Installer/cydia) Renames apps 
- Respring (cydia) Resprings apps Website
- Safari Download Control (cydia) Download stuff, with Safari
- ScummVM (cydia) Play old school games Website
- Scrobble (cydia) Scorobbles stuff somewhere with something 
- SMSNotify (cydia) vibrates your phone periodically when you have an sms 
- Snapture (cydia) camera application Website
- Snes4iPhone (cydia) SNES emulator Website
- Springboard notifier (cydia) notifies SB that app was changed 
- SwapCameraRoll (cydia) swaps cameras roll
- SwapTunes (cydia) lets you have 2 music libraries Website
- SynchStep (cydia) adjusts your music to your walking pace Website
- Talking Alerts (cydia) Talking alerts for SMS and mail etc
- Tapdial (cydia/installer) Adds one touch dialling Website
- TextReader (cydia) View TXT and PALM Doc format.
- Tivo Remote (cydia) A TIVO remote
- TuneWiki (installer) Media player that automatically downloads lyrics Website
- Whirlwind 21 (cydia) Solitaire
- Wifi Toggle (cydia/installer) A Wifi toggle
- WbApp 0.32 (cydia) A WinterBoard theme displaying/modding application
- Wiki2Touch (partially working) Website
- WinterBoard (cydia) Open Source Summerboard Website