Important Links
Pokemon.com
Might as well start off with Nintendo's official pokemon site. 3nodding
Bulbapedia
The most useful resource for any questions you might have about basic game information. Think of it as a Wikipedia focused exclusively on pokemon.
Smogon
The Smogon community is a pokemon community focused primarily on pokemon battling strategies and information. There are many usable designs suggestions for practically any pokemon you would want to use. Many of the rules we encourage in this subforum were picked up from this community.
--Pokemon Designs (Contains pokemon design ideas)
--Stark Mountain (A subforum for talking about Diamond and Pearl.)
Serebii.net
Another excellent source for viewing pokemon stats from a distance. It also includes great information about various games and is generally quite great at keeping up with pokemon-related news.
--Pokedex
--Attackdex
--Stat and IV calculator
--Obtaining free Electivire and Magmortar from Pokemon Battle Revolution
Pokecharms
Another site which keeps up on news but, most importantly, they host a Trainer Card maker. You've maybe seen trainer cards from their site used in various signatures here on Gaia.
--Trainer Card Maker
Useful Links
GameFAQs Pokemon FireRed FAQs
GameFAQs Pokemon LeafGreen FAQs
GameFAQs Pokemon Ruby FAQs
GameFAQs Pokemon Sapphire FAQs
GameFAQs Pokemon Emerald FAQs
GameFAQs Pokemon Pearl FAQs
GameFAQs Pokemon Diamond FAQs
GameFAQs Pokemon Battle Revolution FAQs
(Other GameFAQs Pokemon FAQs can be found here)
Battle Tower Pokemon (Lists details on all the pokemon you battle in the Battle Tower)
Battle Tower Pokemon (Lists details on all the pokemon you battle in the Battle Tower, easier to read, IMO)
Pokemon Elite 2000 Sprites (Contains lots of game sprites)
Pokemon Team Builder (A tool which shows your team's weakness)
IV breeding probability calculator (refresh until it shows up)
Shoddy Battle (A pokemon battle simulator)