I've been playing since the HGSS on format, and over that period of time, theres plenty of decks that have been favorites of mine.
Lets start off with CMT(T). To think Celebi Prime only costed about 3 bucks before Mewtwo EX's release is absolutely insane, and to think that a single card could reach prices of 70$ at the time was practically unheard of at the time (for me at least, of course im speaking about Mewtwo EX). Once Dark Explorers came out, terrakion became an even more amazing addition to the deck, as well as Tornadus EX. It was truly a powerhouse, and was my first (and obviously one of my favorite) competitive decks, due to its near unlimited damage output.
After the BW-on rotation, I played Darkrai EX decks for the next two years. I still play turbo darkrai in expanded to this day, and if I had to pick any deck out of the three I'm mentioning, turbo darkrai has to be my absolute favorite. With cards like Max Elixir, Dark Patch, and Computer Search, it really is possible to hit numbers like 180 by turn 2, and the deck honestly seems to have everything perfect going for it! Keldeo EX helps solve the ever-annoying laserbank, hoopa ex is a great tool to start setting up, shaymin ex for draw support, as well as yveltal ex and both baby yveltals (I only run Keldeo EX and a single copy of Fright Night yveltal, although I do love oblivion wing yveltal). To tell the truth, theres very few pokemon that have been printed in my time as a player which have had a lasting impact on every metagame since their release. If I had to list any, other than Shaymin EX, I would without a doubt say that Darkrai EX has been the most impactful pokemon printed since HGSS. Thats just my opinion though, in no way would I want to discredit cards like Mewtwo EX NXD, Keldeo EX BCR, and Seismitoad EX *shivers*.
In the BCR-on format, I ran variants of Big Basics, even up until XY was printed... where a "Big Basics" deck won nationals. EVERYTIME I see that article explaining how "Big Basics" won worlds, and how Raichu from XY Base was a valuable part of the deck, I cringe. ITS CALLED BIG BASICS FOR A REASON!!! Truly though, Landorus EX is a monster. Not to say that I exclusively ran Big Basics though, I also experimented with Landorus Bats, and I still have a xy-sts version of Lucario Bats which is very very very fun to play.
In the XY-On and up until Breakpoint was printed, I ran Seismitoad Giratina. I still play this deck in expanded at times, where cards like laserbank, computer search, and now special charge, make this deck even better. Once breakpoint was printed, I immediately started playing Darkrai Giratina Garbodor. After a month of running many different variations of the deck, and a lot of tweaking, I emerged with a list only 3 cards away from what the Juniors world champion used. Those differences were a 4th DDE rather than a 10th Dark Energy, a third Darkrai EX over a second baby yveltal, and 2 Parallel City rather than a 1-1 split with Reverse Valley.
Anyway, as I said, if I had to pick any one favorite deck, it would be Turbo Darkrai. Since the deck emerged in Dark Explorers, all the way to its modern variations, I've been running and have fallen in love with this deck.