to those new to the jailbreak scene, here's a list of great Cydia apps that i personally find as must-have apps to install after your freshly jailbroken iphone is unshackled from its former self even before you start installing some itunes appstore apps.
at the end is a list of desktop software for all your iphone management needs.
The Cydia-installed Applications Start-up List/Kit for Firmware 3.1.2 / 3.1 / 3.0 / 2.2.1 / 2.2
must-have apps for FW3.1.3/3.1.2/3.1/3.0:
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 - install this package if you jailbroke using Blackra1n. This 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 - 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.
7) Insomnia - launching this app enables the wifi to continue runnin even when the iphone is in stand-by/suspended state. an "on" badge/notification will appear on the icon when the app is turned on.
8) MakeItMine - change your carrier name into whtever you'd want it to be.
9) Cycorder - a free video recorder for the iphone that records and encodes the videos on-the-fly complete with audio.
10) Chronus - lets you create backups of any of your default apps (contacts/calendar/sms/notes/safari bookmarks/etc) as well as data of the 3rd party apps from the appstore. this app saves inside the folder that get's backed-up when itunes creates a backup of your unit during a sync; very useful when you accidentally delete a contact/sms/notes/etc or when your database suddenly becomes corrupted. this is a paid app but the free trial lets you make 1 backup each per category. more info about it
on this tutorial thread.
11) Emoji - enables the built-in emoji and smileys on the iphone fw2.2 and above. see
this thread for more details
12) 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
13) Lock Calendar - this package displays a list of your calendar events/appointments on your lockscreen. you can even scroll through the list for even further dates. everything can be configured to your liking via a lockscreen settings area on the settings app.
14) QuickLock - tapping the app icon puts the iphone to standby-locked mode, a true 1-tap solution to lock the iphone without using any hardware buttons.
15) aDownloader - download manager app, fully compatible with iPhone/iPad. Browse the web and download files right on your iphone with no iphone SDK restrictions.
16) MobileTerminal - command line/terminal for the iphone for manual non-GUI mod methods.
17) Lockscreen Clock Hide
(link) - puts a setting in the settings app if you want to hide the lockscreen clock and date
18) xGPS - free project aiming to bring a powerful and easy to use navigation software with turn-by-turn directions, vocal instructions, offline maps support and even more. you can download your maps using your desktop and transfe rthem to the iphone for offlime viewing. more info on their
official site.
19) Fontswap - changes your system font as well as your notes/dialer/calculator fonts as well.
20) Maps Enhancer (fw3.0+ only) - provides more options to Maps application: zoom limiting and cache keeping. It is useful for using Maps application offline, with local cache. More information
on this post.
21) SpotSMS (fw3.0+ only) - this mobile substrate extension adds the ability to use the iphone's Spotlight feature to include the Messages app's entries on the search results.
22) SMS Helper (fw3.0+ only) - adds the iphone's missing character counter to the stock Messages app on the "Send" button.
23) OfflineMaps - (manual download and install only - see
official googlecode site lets you copy pre-saved maps into the google maps app for offline viewing on-the-go (no internet connection necessary). more info on how to create pre-saved maps on our
tutorial section. fw3.1/3.1.2 users have to do additional steps posted
on this reply/comment on the official site.
24) Rotation Inhibitor (SBSettings Toggle add-on) - allows enabling/disabling of the screen rotation through the use of an SBSettings toggle.
or
25) iNoRotate - another screen rotation inhibitor which now adds a customizable setting on the Settings app for individual apps.
26a) iShakeLock - a simple mobile substrate extension which locks/unlocks your iPhone by shaking the it.
or
26b) Activator - A common library for activating apps via gestures, buttons and shortcuts. Assign tasks/app launches to specific swipes, iphone shakes, button taps, etc.
27) SprintBoard - Move faster through home screens simply sliding your finger on the springboard page dots like the ABC column in Contacts.
28a) 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
28b) 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.
29) Ringer/Silent Toggle (SBSettings add-on) - ringer toggle without using the hardware switch
Free Desktop Software for iPhone Management
Mac:
1) Diskaid (Shareware only)
(link) - a commercial file browser for your iphone's filesystem that doesn't need a wifi connection. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition) The trial version lets you browse the media partition.
2) Cyberduck or Fugu
(link) - lets you browse through your iphone's filesystem wirelessly through wifi as well as manage/change file or folder permissions and use terminal/command line to execute commands on your unit.
3) Terminal - a command line-based access to your iphone
4) iPhone Explorer
(link) - a free file browser for your iphone's filesystem that doesn't need a wifi connection. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition)
Windows:
1) iFunbox
(link) - a file browser for your iphone's filesystem that doesn't need a wifi connection. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition)
2) Winscp
(link) - lets you browse through your iphone's filesystem wirelessly through wifi as well as manage/change file or folder permissions and use terminal/command line to execute commands on yout unit.
3) iPhonebrowser
(link) - the predecessor of Diskaid that lets you manage your iphone's filesystem without wifi.
4) Putty - a command line-based access to your iphone
5) Diskaid (Shareware only)
(link) - a Commercial file browser for your iphone's filesystem that doesn't need a wifi connection. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition) The trial version lets you browse the media partition.
6) iPhone Explorer (by myPod Apps)
(link) - a free file browser for your iphone's filesystem that doesn't need a wifi connection. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition)
7) iPhone Explorer (by Software4u)
(link) - another free file browser for your iphone's filesystem that doesn't need a wifi connection. this one offers access to the SMS database as well. simply plug your iphone to your computer via usb cable and you're all set. (this also works on non-jailbroken iphones to access the media partition)
8) Total Commander & T-pot plug-in
(link) - another predecessor of Diskaid that lets you manage your iphone's filesystem without wifi. (Total Commander is a paid application which offers a free trial)
there you have it, these are all the great cydia apps that each one of us in the jailbroken community must enjoy having on our beloved iphones.
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