It's also slightly dodgy that you lose karma for, for example, stealing from the Legion when you're fighting against them. It's war, people.
It doesn't have any major effects apart from the ending slides. I know that if you have good karma, Mortimer won't offer his quest to you, and I think there are a handful of dialogue options, but it's really not a big deal.
Losing karma for stealing from the Legion I can sort of see, as while they may have brutal methods, we know that not everyone there is truly evil (you could be stealing from the slaves instead of the masters, after all). Losing karma for stealing from the Powder Gangers - convicted criminals actively pursuing further criminal endeavors - is very shaky to me.
There is only one really noticeable effect from karma that I have seen aside from minor quest hooks (most of which can be gotten around with a speech check of some kind) - you will lose one companion permanently if your karma goes too far in one direction.