How Little We Know is a good one. If you play it right you get a Pimp-Boy so it's my favorite. Brotherhood quests are interesting to. Some people may have killed the Brotherhood before they got a chance to do some of these quests.
No. The absolute BEST Quest is I Could Make You Care. Because if you bothered to get all the tech you have a pretty impresive arsenal no matter what
Beyond The Beef (given by Mortimer at the Ultra-Luxe) requires a lot of thought and many different options are available.