I've sided with all four factions, but after a huge amount of humming and aahing and slapping myself in the face, I went with the NCR in my first playthrough. They were dicks too and I didn't like them either, but out of everybody you could align with, I thought that choosing NCR would probably result in the most happy/decent endings for everyone. (I looked up the endings on the Fallout wiki later, and my assumption was more or less right.) That, and I figured that the NCR would be able to pull their shit together more once they had the Legion off their back.
I Can't Believe It's Not Andrew Ryan Mr. House was my first choice originally, but even though I liked him (seriously, was the snowglobe obsession anything other than adorable?), the more I advanced through his questline the more I was put off the idea of him running Vegas. He seemed like too much of a control freak, overly-nostalgic, and I disliked how he planned on running the entire place more like a business (e.g. ignoring Freeside because where's the profit in helping drunkards and chem addicts?). But the exact moment he turned me off was when he started all that babble about space colonisation. What?? All right, I can kind of get behind the autocracy and the capitalism boner, but space colonisation? You mean this planet's fucked, so let's go fuck up another one? Okay then, Newt Gingrich, but you can get someone else to help you out with that.
The only group that was always out of the question for me was Caesar's Legion. Caesar was one of my favourite characters, but I thought the overall faction was slightly disappointing. I know that each choice is meant to be morally grey, but the Legion's disadvantages so outweighed the advantages -- especially in comparison to the other factions -- that it bordered on ridiculous. They're definitely the token "bad guys" in the game, at least to some extent. Also, aside from Caesar, it felt like not much effort had been made with the other characters. I always forget his name, but Whatshisface who has enough swag to walk up to you in Nipton wearing a dog hat and sunglasses springs to mind: it felt like the references to his disobeying orders in the past and being capable of independent/creative thought would go somewhere, but it never did.
Jesus, that was more text than I'd intended. Whoops.