apt-get install Install a package. If there are dependencies, you will be prompted to continue.
apt-get remove Uninstall a package
dpkg –l Lists all installed packages
respring Respring your device from the command line
A couple of things to note is that for install and remove, you can list multiple packages separated by a space. When searching, the beginning of each line is the package name. Sometimes it will be a single word, though usually it will follow the pattern: com.companyname.appname.
Even if you only ever plan on using Cydia for managing your packages, I would highly recommend installing Apt (along with syslog). Ever installed something that really screwed your phone or been stuck in a reboot or respring loop? I know I have, and it’s no fun. If you’ve got Apt at your disposal you can connect via SSH and remove the offending package if you know what it is.
Cydia Install On Iphone
How To Install Cydia Apps
Otherwise you can do the old tail –f /var/log/syslog and watch for clues as to the which app is responsible. The source for this hint is iPhone World; it's been extremely helpful. [crarko adds: I haven't tested this one. I don't jailbreak so I don't test these.]