http://z14.invisionfree.com/The_Fanfiction_Forum is a dedicated forum for many popular anime fanfictions, you may find this to be what you were looking for.

 

I read decent Sailor Moon Crossovers in that forum. Loved'em.

 

it was actually that site that originally rec'd me to Neon Exodus Evangelion. Mega crossover with a marty-stu, but still very good. The crossover list from tv tropes says it has these:
* 2001: A Space Odyssey * Ah My Goddess * The works of Dutch mystery writer A.C. Baantjer * Babylon 5
* The Blues Brothers * Doctor Who * Emergency! * Firefox * Full Throttle * Ghostbusters * Half-Life
* In Nomine * Iron Man * The Judge * The Man From UNCLE * Marathon 2: Durandal * Men In Black
* Paradise Lost * Pink Floyd * Real Genius * Sailor Moon * SportsCenter * Star Wars
* System Shock and System Shock 2 * Tech Romancer * Tempest * Terminator * Thunderbirds
* Titanic * Tomb Raider * TRON * Uncle Buck * WipeOut * X-COM * X Files

The primary crossovers being Evangelion / X-COM (Yes, the epic game from the 90's X-COM)