You're going to have to deal with a couple of problems here. First, you have to deal with the general (and largely stupid) bias, as you acknowledge, against calling anything humourous "mature". Then you have to deal with the fact that animation has its own history. This second one is very important because it makes it hard for people unfamiliar with the medium to pick out mature content. People see something like Aeon Flux and, because it has guns and lack of clothing, assume it's immature when in fact it's playing off of the existence of those things in the medium. This doesn't mean that it's impossible to convince someone of the maturity of these things, but it's much, much more difficult than looking for things that would be considered mature in any medium, but just happen to be animated. Personally, I'd find this latter option less interesting, but it's worth bearing in mind.
You're also going to have to deal with the fact that a huge amount of western animation has very strong ties to eastern animation at this point. There are series that do all of the work save animation in the west and use eastern animation studios and there are an increasing number of wholly western productions that are done in the style of eastern animation. The lines between these are really blurring to the point where I'm not sure just how fruitful it is to try to draw this distinction.
Some easier ones:
Triplets of Belleville.
A Scanner Darkly
Mary and Max (if you consider claymation animation)
Persepolis
Some harder, potentially more medium-dependent (and, to me, more interesting) candidates:
Aeon Flux
Batman the Animated Series (Heart of Ice being probably the most important episode)
The Tick (humor, but very clear deconstruction of superhero cartoons)
Boondocks (humor, but regularly deals with very mature social questions)
Venture Brothers (humor, but very clear deconstruction of, well, everything - prominent theme of failure)