TicTacToePony (Art, backcards, G1 UK pony ID and MLP Activity Club history. Not sure when last updated but has a Flickr folder of ponies for trade from 2006)
Tabby's Dream Valley (Fakie Spaceman's old site. Stories and comics. Last updated I think in 2006)
Whimsy's Place (Art, customs, photos, etc. The usual. Last updated 01/12/05)
DS Scully's Pony Files (Bad traders list and info on variations and international ponies. Last updated sometime in 2000, I think)
Morning Glory's Garden (Graphics, adopts, low-res recordings of the 80s show. Don't know when it was last updated but the Wanted page mentions the "new 1999 ponies", so.)
Megan Sawyer (This one's not a pony site anymore but apparently she used to make gothic custom ponies and now her site is a portfolio of her work for Bethesda, which I think is neat)
Web Resources
This post I made on the MLPTP (Goes into the basics of website creation. Not a great guide, mainly me rambling, but you can look at it if you want.)
W3Schools (A great resource with tons of tutorials for just about any language you could want)
Zonelets (A blogging engine. I know almost nothing about it but it advertises itself as allowing you to "create an UNPROFESSIONAL-looking website by writing NUMEROUS lines of code" so I'm already sold)