I’d like to note that the majority of the apps below are free, though the paid apps have been legitimately purchased. Support the developers you dirty pirates! I’d also like to note that I do not use any themes (expect iRetina, an SBSettings theme) as I enjoy the look of the default iOS interface.
AndroidLock XT- Use the popular Android lockscreen lock on your iPhone/iPod Touch.
AppBackup- Adds the ability to backup and restore app data for apps from the App Store.
App Switcher Brightness- Adds a brightness slider to the task switcher.
AutoLock SBSettings- Adds a toggle to SBSettings to easily enable/disable AutoLock.
Covert- Private Browsing in Safari. ‘Nuff said.
Fast Copy- Removes the UI delay when using copy/paste, making it feel much snappier.
Find In Page- Adds a bookmark to Safari that, when launched/clicked, allows you to enter a search term and then highlights all instances of the word on the current page. Will become obsolete when 4.2 is released.
Five Icon Dock- Adds a fifth icon to your dock. For more icons, check out Infinidock.
Frash- Adds flash support to Mobile Safari on newer gen iDevices.
FullScreen for Safari- Turns Safari into a multitouch browser with gestures and fullscreen mode.
HDREnabler- Enables native HDR on the iPod Touch 4G.
iFile- File manager to navigate through the file system.
Installous- Allows you to download paid apps for free. *I strictly use it for testing apps before deciding if I want to purchase the app. Installous should not be used for any other purpose.*
iRetina- A super sexy, high resolution theme for SBSettings.
No Bookmarks- Disables the Bookmarks/History popup when Safari is launched without any previously opened tabs.
NoCyfresh i4- Disables Cydia’s auto-refresh that runs every time you launch Cydia.
OpenSSH- Enables SSH access to the file system.
Remove Background- Removes/ends all apps in the task switcher and ends all background processes.
Remove Background SBSettings- Allows for quick access to Remove Background from SBSettings.
Safari Download Manager- Adds a download manager to Mobile Safari.
SBSettings- Enables quick access to common system toggles (e.g.: Brightness, WiFi On/Off, etc.).
User Agent Faker- Allows you to set the desired user agent for Mobile Safari from Settings.
YourTube 2- Download movies directly from Youtube.app and add them to your iPod library.
Other notable apps:
Infinidock- Add as many icon as you’d like to your dock. Paid alternative to Five Icon Dock.
Infinifolders- Surpass Apple’s limit of 12 apps per folder.
IntelliScreen- Add Widgets to the lock screen.
iRemix- Add favorites, bookmarks, quick add and search, song information, and enhanced fast forward and rewind to iPod/Music.
Gridlock- Freely position app icons on SpringBoard.
Shrink- Reduce app icon size to add more icons per line.
Wi-Fi Sync- Sync with iTunes over Wi-Fi.