These pony sites are divided into basic categories. 
Most sites cover lots of different subjects so please, visit all of them! 

General Pony Info:

Dream Valley - A Collector's Guide to MLP, pony identification, checklists, list of released ponies, + more

MLP Collectors Site - MLP pricing guide, checklists, pony poll, art, MOC pics & more

Ponyland Market - G2 (1998 - 2002) Pony Id and more

Lofty's Plush Paradise - Info on Plush ponies w/ pictures - site is down

International/Variant/Nirvana Sites

Mio Mini Pony - Italian Pony Site, Italian pony id & pics

The Italian Resource - Id & info on ponies made in Italy

Sea Pony Cove - link to Argentina pony id & info

Mexican Pony Paradise - id & info on Mexican Ponies

Alternate Birthflowers - info & pics on Alternate Birthflower Ponies

Baby Blumen's Ponyland - pics

Sale/Trade Sites:

The Haven - Skyesurfer's page - sales

Jewel's Dream Box - Jewel's page - sale/trade page, art & more

CyberSunbeam's Pony Site - CyberSunbeam's page - sale/trade, art work, customs & more

Firefrie's Fiery Autumn - Firefrie's page - sale/trade, art, adoptions

My Little Pony UK - a United Kingdom located sale site

Squirtsquirt's Ponyland - sales

The Toy Den - Wolfchick's page - sales, art work, customs

Tic Tac Toe's Pony Page - sale, customs, fun stuff

Fiona's Feedback Forum - THE place to check sale/trade references

Chat Boards:

MLPTP - MLP Discussion, General Discussion, Customs, Sale/Trade

MLP Arena - pony chat

Encyclopedia MLP - G3 (2003+ ponies) discussion and more

My Little Pony Playhouse - more pony chat

Cleaning Tips / Custom Tips:

Emerald Valley - deflocking tips, flocking cleaning tips, pony screen savers, + more

Ribbons & Rainbows - customs, cleaning tips, pony horror stories, free pics, + more

The Custom Zone - customizing supplies & info

Fun Stuff:

The Truckstop - pony games, pony personality quiz, for sale/trades, crafts, + more

World's Apart - Lunacat's website - art work, wallpaper, adoptables

Pebbles the Fakie - Fakie Tour

Misty Mountian - adoptables, art work

Aquiliea's Plushies - hand made plush ponies

JLM's Craptacular Website - take a look!

G2 (1997-2002) Pony Pages:

Rainbow Forest - G2 info

Ponyland Market - G2 info

G3 (2003+) Pony Pages:

Ride The Rainbow - G3 Pony Guide, checklists

My Little Pony Official Site - Hasbro's site for the NEW line of ponies (G3)

Webrings - please see my Mane page for the MLP webrings I belong to