Personally, I loved "Come Fly Away With Me" in my first playthrough, but upon replaying, I realized it felt kind of repetitive and inessential. I ended up skipping it because I knew where Benny was headed, and was eager to get to the strip. I didn't really care much about Manny Vargas's problems, so I headed on to Boulder City and dealt with the Khans. I suppose I might have been able to skip that too, but for some reason that one feels more essential to the plot to me.
I also feel the need to deal with Nipton, one way or another, even though it's not really story-central...
What about you? What do you feel like you're better off skipping, and what do you feel like you just have to do?