It's a really good question.
For me, I think it's an overall result of a combination of things:
1.) I've been playing there for many years, and have only had one problem. This was caused by them, and they apologized by personal email. (This wasn't a general software problem, where everyone is involved. It was just me.)
2.) I complained one day about a member who had an icon of a dog, with a gun to it's head.
They emailed thanking me for the information, and that they would review their procedures, as this kind of thing is what they don't want on their site. They contacted me the next day, and advised that they had contacted the member, and had him take the icon down, or he would be banned.
3.) (but really #1) Honesty, and integrity Except for the usual crying, and whining about "bad beats", and "rigging", I have never seen any serious accusations against PokerStars.
4.) Value tournaments are plentiful, especially on Sunday(s).
5.) Variety of games. They have way more than any other site.
6.) They are pretty transparent when it comes to bots, and cheater software. They provide a list of what is and isn't acceptable
7.) Customer service is quite responsive with personalized e-mails. Unlike
party poker where you get their stock "We're escalating your inquiry".
8.) Payouts are the fastest that I've seen, and I've never had any trouble with them, unlike other site that make you do triple toe loops, quadruple jumps, and sit spins, before you get your payout.
I just have a good overall feeling about PokerStars, and yet, I prefer to play 888, simply because I find it's more fun there.