They have different emphases. I'd use SWN for a more classic space opera type game, and MongTrav for something more like hard sci-fi. SWN's world generator creates a lot of garden worlds with interesting socio-political dynamics, whereas MongTrav generates a lot more marginal worlds with struggling economies.
SWN's char-gen is a lot less random than Traveller's. Some people love the Traveller minigame (I'm one), but you do have minimal control. It's also easier to handle advancement in SWN, since it uses a simple class / level system. Mechanically, SWN is the simpler and lighter game, though there's not a ton of difference in most cases.
I personally think it would be easier to adapt SWN to 40K, which is the main tip in its favour for me, since both groups I'm playing with right now are fans of the 40K setting (I'm running a Deathwatch game next month and I'm playing in a Dark Heresy game right now). Getting them to switch to a more rules-light system would make it easier on me when I'm DMing.
Probably Stars Without Number but only because I can pretty much fit the system in my head and make a good job of running it. MongTrav is an excellent system; I have some of the books and I think that Mongoose have done a terrific job, I just don't think I could do it justice as a ref.
As for which one I'd rather play... Quite frankly I'd happily play any SF game if someone was willing to run it.
TrippyHippy, if your final comment wasn't meant as a dismissal then you should check it out. A 200+ page free download, spend five or ten minutes flicking through it and if there's nothing in there of interest to you delete it. I love it.
Maybe I'll marry MongTrav one day, but SWN smokes and drinks and is a bad, bad girl... or something.
Sorry. I use both. Rules from Traveller, my own small setting and all the advice, the sandbox rules, the factions, alien race creation and world tags from SWN to turn my campaign into a wonderful sandbox environment.
I use both.
From a rules perspective Traveller. But if I wasn't so wedded to the game SWN has a really kick ass little system behind it familiar to every player of early D&D.
I'll wait until I've actually had a chance to play Stars before I commit to one or the other for all time, but... Stars is definitely a contender, that's for sure. It's a surprising amount of awesome for free.