There are, actually. Though the hardest thing to come by is one with absolutely no language issues. Most have at least d*mn in them, though for the most part, that's as bad as it gets in the manga I'm recommending.
The first one that comes to mind is Rurouni Kenshin. No sex at all (one "bad guy" is homosexual and androgynous, though much time isn't given to it, just so you know), and language is present, but mild. Definitely no f-bombs, at least not in official translations. It is, however, about a man who used to be a "manslayer" in the Japanese Bakumatsu (rebellion), and though he himself vows to never kill again, there are many people who would like to make him break that vow, so there IS violence. Not one of the things you mentioned that you were worried about, but I thought I'd make sure you were aware.
Fruits Basket is another one. It starts off very light, but gets darker and more mature as the series progresses. Again, very mild language, mainly by one character. No sex scenes, though there are flashbacks to an after shot where you see the characters shoulders and backs, no nudity. A major plot point of the series is that a whole family turns into animals of the chinese zodiac if hugged by members of the opposite sex, and when they turn back...they are naked. Smoke or hair, etc...always obscures anything inappropriate, though in one particular female's case in one panel, it's just barely. It's an amazing story of compassion, redemption and love, and very popular for good reason.
Death Note is another which has a very mature story line, but no sex, nudity, at all. At worst, one character has some skimpy outfits, but that's it. Language is not excessive, but I do believe it's there. It's a very suspenseful story of a high schooler who finds a notebook which will kill anyone whose name is written in it, and the cat and mouse game between him and the detective who vows to bring him to justice is amazing. Since it's about a notebook that kills, the death count is pretty high, but usually the way the Death Note kills is through heart attacks, it's not really violent, per se, for the most part. The last chapter though...does up the violence.
Saint Tail is probably the cleanest manga I've ever read. It's more of a children's story, though I enjoyed it as a 23 year old.
It's about a Catholic school girl who is a kind of Robin Hood character. She's a cat burglar who only steals things that were already stolen, to return them to their rightful owner. No sex, nudity, fanservice of any kind - most of the time everyone is dressed in a Catholic school uniform - though there probably is a little mild language. Nothing above d*mn, though, I'm sure.
Fullmetal Alchemist is still ongoing, so I can't say where it will go from here, but so far, no sex, no nudity. There is mild language, again, though. The ethical and moral questions it raises are very deep and complex at times, and it's very fast paced. Basically it's about two brothers who through an alchemic experiment have tried to bring their mother back to life. They fail, and in the process one brother loses his arm and leg, the other his whole body and has his soul attached to armour. The story is them trying to get their bodies back to normal, helping people on the way.
Hope some of those help!
Oh, and there is another person who asked a very similar question just a few weeks ago. I believe the thread is called manga that has depth. You'll probably find quite a few suggestions there, too.