- Hasbro instructions
The Zoids site itself is long gone, but you can still find the manual for many critters here (including the action figures, and oddly enough, a few Technozoids). Search for Zoids (and have Javascript turned on). - Hasbro's old Zoids site, take 1 (archive.org)
Hasbro’s first Zoids site, back when, as preserved by archive.org. - Hasbro's old Zoids site, take 2 (archive.org)
The other version of Hasbro’s Zoids site, also preserved by archive.org. - Kotobukiya HMM Zoids Official Blog
News and posts about the HMM Zoids line. Sometimes there’s silly stuff, customs, and other fun. - Mercy Rabbit's blog
Mercy Rabbit does the artwork for a lot of Zoids boxes and other merchandise these days, most notably the HMM Zoids. - Mercy Rabbit's Twitter
- Michiro Ueyama's homepage
Ueyama drew/wrote the CC manga, which ended rather adruptly. He has a continuation online, which The Iron Bible has translated. - ShoPro's Zoids anime site
Covers all four series, and has a number of nice Flash-based galleries of the CG models involved. - Takara-Tomy's Zoids Official Site
Tomy’s official Zoids site. This time around, it’s updated for Zoids Original and the MSS line. - Takara-Tomy's Zoids Ultimate Web
Tomy updated their Zoids site for Rebirth Century, and for now the content for it is still online! - Tomy's Zoids Tactics site
Notable mostly for the character profiles, which feature a lot of battle story people—Tactics is another one of those “smash universes together” games. - Tomy's Zoids Versus site
Good for character references and such, if you dig the Rottiger and Blue Unicorn dudes. 
Is an official shop-type thing. It unfortunately only ships to Japan, but once ran a number of contests.