Akismet works perfectly well with trackbacks. And it learns too, so just mark them as spam and get on with life.
If Akismet isn't enough, I suggest installing Bad Behavior as well. It made 90% of my spam (of all kinds) simply vanish. It's a wonderful plugin. With BB and Akismet, you rarely get any spam at all, and those you do get are caught by Akismet.
Actually, come to think of it, I think Bad Behavior may be the reason a lot of this spam isn't picked up by Akismet. See, Akismet works by getting the spam sent to it by the various blogs using it. But Bad Behavior straight up blocks an incredible amount of spambots. So all this spam blocked by us Bad Behavior users isn't getting sent to Akismet at all. It's something to think about, certainly.