SBSettings: a dropdown toggle menu for many features to save time and efficiency so that you won't have to go to Settings and navigate tab after tab to turn off your Wifi, lower your brightness, turn off data, toggle vibrate, toggle SSH, etc, etc. Also has a built-in process feature that allows you to clear up your memory and to end the process of apps (esp those that are frozen)
iFile: Basically allowing you access to your root files and such. You can manipulate them in certain ways. Allows you to move files in and out of your device and place them in certain directories for certain purposes and such.
MobileTerminal: It's like the Terminal in Linux and the Command Prompt for Macs. It allows you to run certain lines to do certain things. This is more towards advanced usage and such.
Activator: Set gestures to activate certain actions to happen, like you can slide from the bottom of the screen up to close an app, or to open up Angry Birds, or double press the home button to make your Phone.app pop up. There are quite a few possibilities there. Gestures from the device's buttons and on the screen and such, and there's a compiled list of items that you can cause the phone to do with the action you assign them to.
Winterboard: Theme-ing. Download or create themes, put them into your device, use Winterboard to "use" them.
Safari/Chrome Download Manager: Some files or clips and such that you can view on your browser, if you tap on them, before it goes straight to playing, it'll display a screen that asks you if you want to download the clip or whatever, or do you just want to watch/listen to it. Basically it allows you to download things.
Auxo: Just a new look to the device. By default if you double tap the home button, you'll bring up Apple's iOS "processes". Instead of just showing the icons, Auxo will show you a slightly larger icon with the appearance of what's actually on the screen before you left it.
IntelliscreenX: Revolutionizes the Notification Center. It adds a TON of other things that you can do directly on it. Accessible in the Lockscreen and anywhere else.
PKGBackup: Backs up EVERYTHING on your device. This is probably one of the best apps that you'll ever buy from Cydia. It backs up everything on your phone that needs backing up and you can backup your device in iTunes and this little backup package will be carried over as well, or you can manually extract it using SSH (Secured SHell connection)
Action Menu Plus: You know that little menu that you get when you tap and hold on to a word or something? The little menu with Copy/Paste, etc. Well this expands it, giving you other options as well like post on Facebook, copy to Memo, etc etc. Very handy.
BiteSMS: Enhances your texting experience. One feature is that it allows you to reply to texts without exiting what you're doing. A little prompt will pop up and all you'll need to do is tap on "Reply" and you can reply on the spot.
OpenSSH: Probably one of the cores of jailbreaking. It allows you to remotely root your device using FTP (file transfer protocol). It's basically iFile but instead of manipulating files from your device, you manipulate them from your computer using an FTP client like WinFTP for Windows or CyberDuck for Mac. There are also applications like iExplorer or iFunbox that does this a little more "efficiently". Instead of doing it through Wifi using SSH; iExplorer and iFunBox uses the USB, meaning faster transfer speeds, and neither iExplorer nor iFunBox requires a jailbreak, so just a heads up if you end up with an unjailbroken device and such. OpenSSH and these 2 applications allow you to root your device like you do on an Android and such.