My Little Ponyland- Guide for all three generations in an easy to browse format categorized by year
Soft Flock- Carries 30 or so colors of flocking if you are so bold as to want to try flocking a pony
Restoredoll.com- Carries several hair colors that are close matches to the original pony hair. Also has a color guide with photos comparing their hair colors to actual ponies
Dollyhair.com- Similar to restoredoll.com in that they carry colors specifically for mlp's and have a color guide with pictures of the original ponies
My Little Pony Arena- Has a wealth of pony information along with forums on just about any pony topic you can think of, and then some. There's also an area to trade or buy ponies, a place for customs, artwork, and a lot of other extras
Aves Clay and Mache- a lot of people use their Apoxie Sculpt for their customs
DoctoredLocks- The silky straight kanekalon braid is good for pony hair
Pony Price Guide- Average completed Ebay auctions, very handy for pricing your ponies but I wouldn't go solely by these prices as some are a few years old
The MLP Preservation Project- Excellent resource for restoration advice including cleaning, re-hairing, styling, whitening and lots more
My Little Wiki- Resource for info on all generations of MLP
Ponyland Press- Another G1 MLP resource guide with lots of fun extras
MLP Hair Color Guide- list of hair colors for mainly G1 ponies corresponding to Dolly Hair and My Little Customs