I submit the following: James Castle, a Harry Potter/Punisher fanfic, Gods of Light and Dark, a Star Wars/Stargate/a bunch of other series thing, the Legacy of the Red Sun trilogy, Star Wars/Superman and its sequel, Children of the Red Sun. All on fanfiction.net. Also, The Best Seven Years, a Calvin & Hobbes/Harry Potter fic.
Hmm…
I would like to say Pokegirl, because it turned out to be a lot better than I expected when I started reading it, but it’s neither on ff.net nor is it actually GOOD. 
I haven’t trolle-err, VISITED ff.net in so long that I can’t really remember anything that would fit within those criteria. (Some crossovers, but they’re bad. Some good fics, but they’re not crossovers.)
X-Men Vs. Street Fighter.
Blood Omen: Legacy of the Harvest Moon.
Spring 1: Spent the day meeting my new neighbors. No real way to avoid it. Got strange looks when I told them about the vulture coop. Maybe I’ll try chickens instead. Grandfather left early this morning, leaving behind nothing but a note: “Beware the ides of March.” I’ll add that to my to-do list.
Spring 2: Pulled a late night clearing the field of stones. Also found a few skulls. Locals assured me they were mole skulls. Seems that moles were bigger in these parts.
Spring 12: Maria resisted my attempts to drain her blood and devour her soul. Her holy aura kept my hunger back. Try Nina tomorrow.
Spring 27: Found the legendary blade Potato Reaver. Reaved my potatoes. They all burst into flame and turned to ash with a single swipe of my blade. Needed to clear field for corn anyway.
Fall 13: Anne made a stake gun and stalked me through the fields of dying corn. Managed to escape by sic’ing the zombie chickens on her. Will have to do something about that girl.
Your feeble attempts to defeat my vast powers are in vain, you mortal fools! MUHAHAHAHAHA! poses
Ah yes, good old Legacy of the Harvest Moon.
Legacy of the Harvest Moon was actually a pretty good read.
Forget Umah. Maria the closet goth was a much better queen for Kain!
I can’t find it right now, but I once read a great Superman/Tenchi Muyo crossover. The person who wrote it obviously knew the mythology of both series well (he used the original version of Tenchi, I believe, and the Superman from the 90’s) and came up with lots of interesting ideas- like having Kryptonians and Jurayians be related, Ryoko and Superman having a small moment over the fact that they were both the only members of their races, Mihoshi mistaking the Justice League for “The Super Friends!” and Washu pestering Superman like a high-tech version of Mr. Mxyzptlk. VERY well written too.