FF.net's archive as of February 18th, 2010:

[behoimi]

(Thank you, FF.net, for keeping track of the popular fandoms that much easier. With the earlier entries I tallied up the results myself, fufufu.)

Game fanfiction:
1) Kingdom Hearts (50,002)
2) Final Fantasy VII (30,142)
3) Pokemon (29,669)
4) Sonic the Hedgehog (17,232)
5) Legend of Zelda (15,317)
6) Final Fantasy VIII (11,838)
7) Resident Evil (6,449)
8) Super Smash Brothers (5,446)
9) Tales of Symphonia (5,337)
10) Fire Emblem (5,270)
11) Final Fantasy X (5,172)
12) Harvest Moon (4,395)
13) Mega Man (4,306)
14) Mario (3,662)
15) Halo (3,488)
16) Final Fantasy X-2 (3,417)
17) Phoenix Wright: Ace Attorney (3,005)
18) Devil May Cry (2,976)
19) Final Fantasy IX (2,844)
20) Warcraft (2,642)

Anime fanfiction:
1) Naruto (226,370)
2) Inuyasha (91,807)
3) Yu-Gi-Oh (50,652)
4) Gundam Wing/AC (40,242)
5) Bleach (37,460)
6) Digimon (32,930)
7) Dragon Ball Z (31,729)
8) Sailor Moon (31,477)
9) Fullmetal Alchemist (30,186)
10) Card Captor Sakura (23,433)
11) Yu Yu Hakusho (22,760)
12) Death Note (20,937)
13) Beyblade (19,142)
14) Prince of Tennis (16,946)
15) Rurouni Kenshin (15,903)
16) Fruits Basket (15,587)
17) Ranma (10,441)
18) Ouran High School Host Club (10,334)
19) Shaman King (8,982)
20) D.Gray-Man (8,841)