Here is my list of must-have apps for Firmware 4.x (not in order of importance)
Credits to m.o.r for opening this thread, by the way i copied some of the app descriptions from his post on the first page of this thread
1) Winterboard - a powerful skinning app that lets you apply themes on all parts of your iphone's GUI (it comes with a few themes but individual themes/skins are installed separately from cydia)
2) AFC2ADD - iThis package enables you to use desktop software like iPhone Folders, iPhone Explorer, and Diskaid to browse through your iphone file directories while the unit is connected via usb cable to your computer.
3) openSSH - a back end process to enable wireless access to your iphone's files through SSH using the desktop's WinSCP/putty for windows & terminal/Cyberduck/Fugu for macs.
(Note: Make sure you have secured your iPhone and changed the default root/mobile password prior to installing this unless you want your files to be widely accessible to the public 
)
4) SBsettings - this is the evolution of the infamous bossprefs app. to view the toggle switches, simply swipe your finger from the area in the statusbar's time/battery downwards or sidewards to pull-down the toggle menus/hide/unhide apps settings. the toggle menu will appear even when any app is still open and running on screen! there have been a lot of additional SBSettings toggles that have been released ang among the best ones are: keepawake, autolock sbsettings, volume slider, close button widget, fakeAPN, etc. these are installed separately.
or
Bossprefs - gives you good toggle switches for SSH/edge/3G/airplane/bluetooth/etc for direct access, hide/unhide apps from the springboard.
5) iFile (paid app) - the best cydia-installed photo, video, audio, document, ebook viewer. support a slew of media/photo formats, and is also an awesome ebook reader that lets you jump pages by typing-in the page number of the ebook/document. it also has a built-in web server feature that lets you upload files from the desktop to the iphone as long as both are connected to the same wifi network. it also manages zip files (create/extract), has a text editor, and has file permissions and ownership changing features. iFile is a commercial/paid app but all the basic features are present in the trial period/free version (contains pop-ups to upsell for the full version).
6) Backgrounder - a mobile substrate-based extension to iphone that allows 3rd party apps to run in the background (applications are normally terminated upon returning to the springboard), see the app's cydia "more info" for intructions on how to use. installing this will not add an icon to the springboard.
(updated and included auto detect function for ios 4.x)
7) MakeItMine - change your carrier name into whtever you'd want it to be.
8) Emoji - enables the built-in emoji and smileys on the iphone fw2.2 and above. see this thread for more details
9) StatusNotifier or Notifier - both apps are different from each other but both offer the same small widget that displays new sms/missed call/silent switch/etc notifications on the lockscreen
10) MobileTerminal iOS4 v 426- command line/terminal for the iphone for manual non-GUI mod methods.
11) Activator - A common library for activating apps via gestures, buttons and shortcuts. Assign tasks/app launches to specific swipes, iphone shakes, button taps, etc.
12) Data Toggle (SBSettings add-on) - a real data toggle that disables/enables the data connection provided that you have setup the proper APN settings of your carrier on the Settings app
or
12b) mDatatoggle (SBSettings add-on) - a better data toggle for OS 3.2 (iPad) and 4.0. this one uses the actual iOS data toggle implementation, not a 3rd-party hack like the one above.
13) Ringer/Silent Toggle (SBSettings add-on) - ringer toggle without using the hardware switch
14) biteSMS - replacement to stock SMS app with quick compose and quickreply functions
15) ultrasn0w - unlock 3g/3gs on any baseband
16) sbrotator (paid app) - rotate springboard including icons, landscape mode enabled
17) mywi (paid app) - share data connection thru wifi, use iphone as modem
18) remove recents - remove apps that dont support multitasking in the task switcher
19) Cydelete - delete cydia packages from springboard
20) LockInfo (paid app) - customize lockscreen to include calendar and other plug ins such as Mail, SMS< Phone, push notifications and many more
21) Youtube fix - install this if you used a hacktivated 4.x CFW in order to access youtube
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