Battle Story & Models - Customizing - Fanart & CGI/3-D
Battle Story & Models
Autocrat Islet has customs, articles, fanfiction set in the battle storyverse, and many other things.- Empire Molga Party
Here’s a site just for Molga! How can you not love Molga? 
Gilvader’s Room has a ton of content, mostly centered around Gilvader, but also including things like a section for the OJR-era video games.
Imagine Forest has clever windup Zoid customs, articles, and various other things of interest—including some scans of and text from old catalogues.- Machine Heart's Zoids collection
Lots of model photography, sortable by era. 
page Z-F has fanfics (battle story and Fuzors at that), thoughts on Zoids, customs, and more.- Planet Zoids
Lightjester’s site. Lots and lots of old Zoid info, customizing stuff (including a lot of awesome work with gears and other motorized things), old catalogues, and pictures of some obscure OJR products. 
The Sacred Galaxy Empire’s Zoids section has lots of battle story and Zoids info (including a very well-done timeline), plus a few custom Zoids and other things.- Zi Matrices
Photographs of tons of Zoid model variants, obscure included, all sorted by type. 
Zoids Awakes has really good Zoids photography, and some great custom Zoids too.- Zoids Dictionary
The name says it all. If you’ve ever wanted to know who character X was and what they did, this is the place to go. It covers everything Zoids in (Japanese) alphabetical order for easy searching. 
Zoids Hanger is full of pictures and info on newer releases, along with a Zoids wiki and other interactive things.
Zoids Ignition has tons of content: reviews, articles, customs, and much more.
Zoids Land has reviews and info on models, games, anime…just about anything Zoids.- Zoids Musuem
A mirror of a now-closed site, full of pics/info on a great many early-NJR Zoids with some old-school of all flavors (not just Japanese) thrown in. Keep a lookout for the all-chrome Shieldy (apparently a Coro Coro prize). 
Zoids Ocean has information on Zoids releases, new and old, with things like pictures and reviews from multiple sources.
Zoids Parallax is home to a wonderful mix of fanart, photomanipulations, and ponderings/articles with an OJR slant.
日々の生活 Life of Every Day is another site with both new and old Zoids (including American lines). Other toylines too!
紗蔚綸那’s Toy Box has a lot of old-school Zoid content, including the box take on the Battle Story and memories of the old line sent in by other fans.
１０年後も好きですか？ (formerly Zoids Corner) has pretty much every model out there, complete with pictures and stats on most of them, and some of the first pics of new releases.
Customizing
Altitude of Mobius has a lot of well-painted Zoid customs, especially using the HMM line. Check out the Three Guards type Saber Tigers!
Code-ta28 has customized Zoids and other mecha.
Nezumi-hanabi has customs, including assorted collab projects and stuff featured in magazines.
Otika’s Room has wonderfully shiny customs, including some people may well recognize – Lightning Saix D+, anyone?
The Private Laboratory of Living Machines has a lot of customs, including a Redler for Wolff.
Tono’s Zoids has customs, photo art/image manipulations, and general model fun. Fun…like Helimolga!
Yaiba has a Murasame Liger custom (naturally), plus some other guest custom Zoids.
Z-Zoo has tons of customs from all different people, organized like…well, a zoo.
Z-Zoo’s Godos x Iguan gallery, because it deserves a link all its own!
Zi Craft Union features the work of lots of customizers. Tons and tons of great work here, all well-oraganized.- Zi-channel -Custom Zoids Gallery-
Is what is says on the tin: a huge gallery of customs submitted by posters on the Zoids section of 2chan. 
Zi-E (Zoids Engineering) has an archive with a great many customs – since 2001!
Zoids All Owners Discussion (formerly Zoids Art of Dirt) is a customizing group including in-person gatherings. Some very impressive dioramas and customs here.
Zoids Epic Electronica has a large custom gallery with both the owner’s customs and those sent in by others.
Zoids Galaxy has gallaries of regular models and customs alike, including an excellent Command Wolf LC repaint.
Zoids Genesis Collaboration: Mugen Liger Vs. Bio Volcano is a gallery for a (very snazzy) custom collab project.
Zoids Hangar-29 is mostly a customizing site (and there are a lot of customs here), but includes fanart.
Zoids Nexus has customs and art to to go with them. Also plays host to many contests.
Zoikino has some really, really nice customs and “making of”-type pages…plus regular model reviews, a diary, and more.
ガブの館 G-Room has some really impressive customs, including Salamanders aplenty and anime-style Zoids.- ツンの作業机
Some really sleek HMM customs and conversions of regular -> HMM kits with a focus on the Geno/BF family and Ligers. Lots of LEDs and lightup bits too! - 名も無き工房
Custom Zoids (including some very clever reworkings and Bio Zoids), kit reviews, and other such shiny things in blog form. - 赤ぶろぐ
RED’s blog of custom Zoids work. It’s no longer updated, but there’s lots of cool stuff to be found anyway.
Fanart & CGI/3-D
Black Maniac features very crisp-looking Zoids CGI with progress shots and wallpaper of the final products.
Zoids CGI art, including Liger Zero armors.
Nama’s CG Room has Zoids CGI (among other things), including some animations.
Object 3D is full of Zoids CGI images—it’s even got some tutorials and in-progress pics.
Poco has fanart of Zoids characters from multiple continuities, plus other things anime and game.
S-Edition has a good selection of slick-looking Zoids CGI pics.
Vision of Zoids has fanart, and lots of it – refined, custom, and original Zoids of all different sorts.- Zoids Oekaki archives
Tons of pics you can browse through. Watch out for NSFW stuff—things on the board labeled 暗黒大陸 (with “dark” in the URL) are often R-18, too, so tread with caution there. 
わんころげ工房 has CGI Zoids (including a great many Saber Tigers), customs, and general model photos.- 生きものZi球紀行
Zoids, gone nature documentary with really cool edited photos. Check out the baby Command Wolves.