"You guys" is a familiar, all-inclusive way of addressing a group of men or women directly. That said, there are some important distinctions you must understand.
"You guys" is more likely to be said in women => women or men => men or women => men or mixed-group => mixed-group contexts. It is less likely to be used in men => women contexts, but is still heard and would probably not occasion any confusion or merriment.
The singular "guy" is another animal. It refers to males. It is also used to draw gender distinctions in a general way.
A guy walked into my store and asked for some cigarettes.
There is no doubt that this is a man we're talking about.
In most plural usages that are not directly addressing a group, this rule also applies.
Guys are pretty simple, when you get right down to it.
This will also be understood to refer to men only. If you wanted to make the same statement about women, you would use another noun: women, gals, whatever.
However, you could say something like
My friends in San Francisco? Those guys are so crazy!
Now we're not sure we're talking about men. If the speaker is female, it might mean a group of women. Note that I say might. It is more likely she would still be talking about men or a mixed group, but you never know.
It's a hard word to pin down. Much depends on context.
Addendum
On a walk yesterday evening I encountered a woman walking three dogs. When we got close the dogs started barking at me. The woman and I exchanged greetings, and then she admonished her dogs by saying: "Cut it out, you guys!" One dog kept barking, and she said: "Sally, stop it!" What to make of this? I suppose that for some people "guys" can refer to groups of dogs as well as humans, and not just male ones. Ain't English fun?
Best Answer
I've certainly only used it or seen it used as a generic, gender-neutral term. (And only in the phrase ad hominem.)
As Kosmonaut mentions, part of it is that it's in a different language, so any gender mismatch* is not going to be apparent to people unless they know some Latin. But there's also the fact that classically, in many languages the word for "man" had two meanings: (1) a masculine person, and (2) a member of mankind; a person (of unspecified gender). Modernly, the second meaning is sometimes seen as prejudiced against women, and thus people come up with all sorts of newfangled constructs to avoid that usage. Thus you get (hopefully**) deliberate plays on words like "ad feminam", which doesn't actually mean much of anything, but is understandable if taken in parallel with ad hominem.
* As JSBangs points out, homo is not actually the Latin word for a specifically masculine person — that would be vir — so there actually is no gender mismatch with using ad hominem when the subject of the attack is female.
** If the usage was not deliberately playful, but meant sincerely and literally, I would find it to be sad evidence of the decline of society.