It's totally fine as long as you're mindful of who you're saying it to, however that might be more of an issue of tone than it is of offending people for using gendered speech.
To break it down, you would be totally fine saying something like "are you guys coming?" to a group of guys, to a group of guys and girls, or even a group of girls. If it's just a group of girls you can say "you girls" or "you ladies" or whatever you prefer, but guys is acceptable.
You cannot use "guys" generally to refer to women in all situations. For example, if you were to say "I went out to dinner with some guys from work" I would assume that it was a group of all men. In fact there are plenty of girls who take pride in being "one of the guys," which means they think they are treated like a "guy" when in groups of male friends.
If you're worried about making a mistake with it, just keep your references to girls as "guys" to the phrase "you guys," and use gender neutral words for the rest. I think that in general that rule should hold true, with anything other than "you guys" having a distinct masculine connotation, with some room for a few exceptions.
10 year update:
Since this question was first answered in 2013 the dialogue around gender and speech has evolved significantly. Although I think the original content of the answer largely still holds, I do also think there is an increased need to be mindful of audience and context. While many, if not most, will still not object to this general usage of "guys," the issue has become highly polarized and you may be more likely than before to come across people who take issue with it and try to police its usage. On the whole, it's still not really a faux pas to use it, but at the same time don't be surprised when HR at work, for example, gently nudges everyone to avoid using it in favor of inclusive gender-neutral language.