Other than Beyond the Beef I haven't found any evil quests or quests with evil options. Any help?

Plenty of quests given by the BoS, Caesar's Legion and I believe the Omertas, which are about as evil as one can get.

At the very beginning you're given the choice of two evil quests/tasks for the Powder Gangers, and many quests that can be considered good have options to take a more sadistic or plain evil route to their completion.

And don't forget Helios One. If you think about long term repercussions of the "evil" choice of that quest, you could be looking at the extermination of mankind. Again.