According to Fanfiction.net, the most popular fanfic crossovers for anime and manga are as follows...
1. Naruto
2. Inuyasha
3. Bleach
4. Axis Powers Hetalia
5. Fairy Tail
6. FMA
7. DBZ
8. Sailor Moon
9. Yu-Gi-Oh!
10. Yu Yu Hakusho
11. One Piece
12. OHSHC
13. DN
14. Ranma
15. Black Butler
16. Soul Eather
17. Hitman Reborn!
18. HSDXD
19. Digimon
20. D.Gray-Man
21. F/SN
22. Rosario + Vampire
23. RWBY
24. Familiar of Zero
25. Vampire Knight
Now, Naruto is at the top of the list with 24,034 stories, but Inuyasha (2nd on the list) has 8,396, a HUGE difference!