Personally, "guys" feels okay to me despite its roots because it feels like it's been "gender neutralized" over the years for the kinds of contexts being discussed here. I say it and I don't personally mind when other people say it. One can probably make the case that "boys" is in the process of undergoing this same transition, but I don't think it's there yet, and I think that's the problem. It still feels explicitly male to me (and to several others in this thread, clearly), and I definitely feel excluded when I'm in a group that's addressed this way.
Like, for example, I'm in a raid team in WoW, and when we narrowly succeed in getting a boss down, someone has started sometimes saying, "Nice job, boys!" and my immediate, instinctual, gut reaction is to feel like, "What, are you saying the girls didn't do a good job? :( " and then I have to stop and consciously tell myself that they probably didn't mean it that way. (Note that nearly 1/3 of the group is female.)
It doesn't bother me to the point that I feel like I need to interrupt the raid to call it out(too non-confrontational, don't want to get the reputation as That Guy), but I definitely notice it and as someone who's already got self-esteem issues I can see that tiny feeling of exclusion wearing me down over time if it continues. If they were to say "Nice job, guys!" instead, it wouldn't bother me a bit. It wouldn't register on my radar as out-of-place at all.