RE: Your Deck Top 3
Since this has been edited to include any deck, I'll post my 2 cents.
1. Plox (HP-on, DP-on, and DP-on season II)
I don't think there's much of a question here. Plox was the most metagamed deck of anything in recent history, perhaps the most of all time. In the Plox format, you either played plox, or you played a plox counter (intimidation, which I will get to later). The deck originated in the Holon Phantoms on era, where it was the most broken deck I have ever seen in my entire life. Turn 1 you used Call Energy to search out two basics, and turn two you would Rare Candy, Gardevoir, Double Rainbow Energy, and proceed to lock your opponent out of powers. This of course is an optimal setup, but it happened quite frequently as Roseanne's Research, Celio's Network, Bebe's Search, and Elm's Training Method all gave you ways to search for the pokemon you want. In addition to extreme consistancy, there were so many different variants it was ridiculous. Furret was the original starter for the deck, although it got phased out eventually. Variants with Uxie, Mesprit, Uxie Lv. X, Azelf Lv. X, and Jirachi EX all existed. THe Plox list that won worlds used both Absol EX from Power Keepers and Jolton* from power keepers, which had been pretty much unheard of beforehand. This deck is also the reason we have time limits in top cuts. I remember a battle roads that didn't end until 7:30 (started at 10 AM) because the top 4 in seniors was Plox, Plox, Plox, and Skittles. (Skittles ended up winning BTW.)
2. Flygon EX Delta Spread (Holon Phantoms-on)
Flygon EX Delta Species from Dragon Frontiers was great in its day. Flygon's poke-body spread 10 damage to each of your opponent's basic pokemon in between turns. It's attack for {P}{P}{C} did 80, and 10 damage to each of your opponent's bench pokemon that already had damage on them. Goal was to get Flygon EX set up quick, and kill things. Since everything went off of Trapinch, regular Flygon with energy acceleration was a good tech in the deck. Fearow from Crystal Guardians and Nidoqueen from Dragon Frontiers could both be used to search Pokémon out of your deck. And Holon's Castform along with Delta Rainbow Energy meant you always had the energies you needed. Rayquaza EX from Dragon Frontiers also gave the deck some much needed pick-off power.
3. Gyarados (MD-on)
I include Gyarados in my top 3 because of the dominance it had in my area. You can thank [member]Pokeman[/member] for making Gyarados a huge part of the meta of the midwest area. Spreading the deck among Team Typhoon and stuff. Credit where it's due, he pioneered new variants of this deck al the time, and while he may not have invented it, he played it great, and created many variations. Variations included Regular Gyarados, Gyarados Counter (a specific Gyarados which was made to counter itself. It used Ditto LA, Mesprit LA, and Judge.), LuxDos (used Luxray Lv. X instead of Pokemon Reversal) and TankDos (not the most successful, but it used Blissey Prime, BTS, Super Scoop up, and Junk Arm to heal damage all the time. Some more nooby variants even included Life Herb with Junik Arm.) Gyarados was an extremely versatile deck, and its only bad matchup was against LuxChomp, which it could still beat if it got set up quickly enough. (To be fair though, if we had longer rounds, DialgaChomp would have a beter chance against it.)
Honorable Mentions:
LuxChomp
It was the BDIF at the time. No questions asked. I think only Plox and Gengar topped this deck in terms of popularity, although that's probably only because Luxray Lv. X was $80+ during tournament time. Free prizes every turn, seldom lost a match to anything not named "Machamp", and even then it had a chance if played with Unown G correctly.
DialgaChomp (Dial Tone???)
Turn 1: Deafen trainer lock
Turn 2: Deafen Trainer lock
Turn 3: Deafen Trainer lock
Turn 4: Warp, Garchomp C Lv. X, Bronzong G the energy over, and PokeTurn. Rinse and repeat. Serious tanking capabilities with Unown G, and multiple special metals stacked. Junk Arm gave you 8 free turns to prevent a KO. Its only loss was that it was slow, and 30 minute rounds was really its downfall. It was one of the best 2/3 decks ever due to its late-game potential for extreme comebacks, but 30 minute swiss rounds weren't helping.
Gengar Variants
SpeedGar. VileGar. GeChamp. MotherGar. They all ran rampant in their respective formats. I played 4 mirror matches out of 8 rounds at my first nats when I used MotherGar. This deck was hard to beat. If you flipped nothing but heads (Cody W I mean you.) it was even harder.
LBS
This was a really creative idea. I couldn't have came up with it. Despite the fact that it only won worlds in Juniors, it was still a cool idea utilizing Blastoise EX (FR/LG), Lugia EX (UF), Steelix EX (UF), and Holon's Magneton/Electrodes to kill stuff. Oh and Latias* or Rayquaza *.
Intimidation
Also won worlds in Juniors. It was the Plox counterdeck that popped up for a worlds showdown. Won Juniors against Plox, and PB member [member]Bonsly1994[/member], head of former Team Renegade Top 16'd masters with Intimidation. It utilized Scizor from Majestic Dawn to put all the Double Rainbow Energies out of play for the entire game, and Toxicroak from Majestic Dawn to OHKO stuff, and maybe Paralyze too. Bonsly's favorite game was his last swiss round when he came back from 1-6 in prizes against Plox to steal the victory 1-0.
This isn't a deck, but Chatot MD deserves a mention. Everybody said this card was a waste of space, and that it was horribly inconsistant as a starter. (It was a 60 HP free retreat card that was a Copycat for 0 energies from Majestic Dawn.) This card won at least one division in worlds every single year it was legal for play.