There are too many stories I've read that I've considered excellent, but I'm just posting a very fantastic crossover I've been reading lately.

Suzumiya Haruhi no Index
Category 1: Haruhi Suzumiya series
Category 2: Toaru Majutsu no Index/とある魔術の禁書目録
Genre(s): Sci-Fi/Humor
Rating: Rated: T
Summary: After discovering the existence of a place named ‘Academy City’,
the SOS brigade have to deal with an unlucky transfer student… one that
might just destroy the universe if they're not careful.
Status: OnGoing
Warning: Novel (Index) and Manga (Railgun) characters not yet featured in the anime are featured.

I myself have written a few, but meh... I won't post the links.