Indie is the most popular choice i think, probably followed by ncr and house. Don't pick legion, its way harder to do the majority of the game with every ncr guy you meet shooting at you, and every follower seems to hate them.
Personally i like doing ncr missions and then backstabbing them to work with the yes-man for an indie vegas, really up to you though.
I'm currently doing a stealth character who works for both NCR and Legion. Really is a Legion spy. As long as you do your killing while sneaking and never do quests that purposely hurt the Legion, you can get away with being friendly to both factions.
But this is Pre-Strip by the way. By the time you are granted access to the fort, you will only be able to do 1 or 2 quests before the NCR brands you a terrorist.