XD: I actually started with Pokemon XD, so the first Pokemon I ever battled with was a Salamence. I evolved my starter into a Jolteon, ditched it pretty early on, and mostly just used Walrein and Aggron, though I'm pretty sure I also had a Swalot, Houndoom, Marowak, and something else on my team. My nicknaming skills were so terrible that such horrific names as "BIGMOUTH2" were quite common, and "FLAME" the Houndoom was one of the very best.
Firered: My second Pokemon game, not counting a used Yellow and Red, which I got at the same time as it not realizing that they were all pretty much exactly the same thing and which I never actually played. My nicknames included such gems as "ZAP" (Raichu), "SUPERPECK" (Pidgeot), and another "FLAME" (Charizard), but at least I managed to keep the numerals out of it for the most part.
Emerald: My third Pokemon game. My main team was about as creatively-named as my Firered one, but I did have several random Pokemon with nicknames that were actually pretty decent because of their sheer randomness, like "MILKSHAKES" the Swablu
Diamond: I believe this was actually the first game that I beat the Elite Four on, even though I probably got it about two years after Firered. It was around this point that I began to realize how ridiculous some of my nicknames were, and thus I kept them confined to my team members and legendary Pokemon. They ranged from bland but decent, like "SKULL" the Rampardos and "SPARKY" the Luxray, to a bit more iffy, like "PLANTSHELL" the Torterra and "TIMEBOB" the Dialga. More recently, I apparently discovered lowercase levels and renamed my main team of six. Those four are now "Yorick," "Leon," "Rupert," and "Chronos," respectively.
Soulsilver: My personal favorite game, and probably the one that I put the most time into. I used the same nicknaming scheme as Diamond, and might nave come up with some good stuff if I hadn't insisted on working the name "Fred" into every nickname I gave. I suppose "LIL'FREGG" the Togepi WAS sort-of cute, though, and "PSEUDOFRED" the Sudowoodo has a nice ring to it. I did a similar re-naming with my main team as I did on Diamond, and ended up with "Fred" the Feraligatr, "Albus" the Togekiss, "Erik" the red Gyarados, "Aurelius" the Ho-oh, "Hephaestus" the Groudon, and I-forget-what-I-named-it the Lugia.
White (first time): Still continued with the same plan of nicknaming team members and legendaries. I have a Samurott named "Fred 2.1" after "FRED #2" the Feraligatr (its original name, since my trainer is named Fred), and a Victini named "Frictini," but I gave up on the Fred names after that. My personal favorite is probably "Norris" the Throh.
White (second time): Lost my original White for a couple of months. Finally decided to go buy a new one. Found the original copy within the week. Probably should have bought black, but on the bright side, it was a used copy, and I got some nice Pokemon including my only Deoxys off of the previous save file. I believe that this was the point at which I started giving nicknames to every Pokemon for the first time since Emerald, (though I could be wrong), which I have been doing ever since now that I trust myself to make most of them not complete garbage. It was also the first time since Emerald that I didn't use any legendary Pokemon on my team, and I generally focused on training interesting Pokemon like Axew and Tirtouga, rather than just throwing random stuff onto my team.
White (third time): Apparently deciding that two playthroughs still weren't enough of the Unova region, I then proceeded to delete my game on my second copy and trade over a team of level 1 Pokemon that I liked to play through the game. I ended up with Vesper the Gliscor, Daxia the Haxorus, Moriarty the Dusknoir, Atlas the Torterra, Gobi the Flygon, and Hugo the Golurk, who now have a place of honor in my signature. Also noteworthy in that I have an entire box of uniquely-nicknamed Elgyem, one of which is the first and only shiny Pokemon that I caught myself. I just wanted an adamant-natured one with synchronize...
Emerald (second time): A particularly fun second playthrough of Pokemon Emerald where I just used rock, ground, and steel types and nicknamed everything after an ancient or historical town or city of some sort. I ended up with Troy the Swampert, Alexandria the Aggron, Memphis the Flygon, Jericho the Armaldo, Pompeii the Camerupt, and Delphi the Solrock.
White 2: Possibly tops even Soilsilver in terms of sheer awesomeness. It's a very tough choice, at any rate. This time, I did something a bit different with my team, rotating twelve Pokemon instead of the usual six. This also added a fun challenge to my game since my Pokemon were usually underleveled, and I ended up training all sorts of interesting Pokemon such as Genesect, Volcarona (Sekhmet), Defiant Braviary (Dakota), and Skill Link Cinccino (Mr. Doom). After beating the game, I added on another six, including a second legendary, Latias (Grace). Between those 18, every type is represented at least once, and I seem to have the most Bug (Leavanny, Volcarona, and Genesect) and Steel (Lucario, Excadrill, and Genesect) types. White 2 also marks the first time that I have completed the National Pokedex (as of yesterday) on any Pokemon game.
In addition to these, I also have a long-standing unfinished game on Colosseum, a horribly-failed Nuzlocke second run on Diamond, and a partially-finished second run of Firered where I only used as many Pokemon as the upcoming Gym Leader had.