After jailbreaking for 4.1, many of you will notice you can no longer run apt-get commands from the command line, whether SSH or MobileTerminal. This is mind boggling, and none of the support sites or forums seem to have the right answer. The most common suggested solution is to delete some sources from Cydia and re-add them. This doesn't work.
After a few hours of troubleshooting, I gave up and assumed it was a limitation of greenpois0n. However, today I accidentally found the answer, and it's quite simple to make this work again.