Top 2 pokemon from each gen.

[Brendino]

I'm going to write down evolution lines (if applicable), because in most cases I don't prefer one evolution over the other.

Gen I
Butterfree line - Butterfree became my most used Pokemon in HeartGold, after neglecting it for so many years. It was also one of my most sought after Pokemon cards as a kid, and my cousin got me a Japanese Butterfree card well before the Jungle set even came out in North America (still have it in my binder to this day).
Pidgeot line - A Pidgeot has always been a member of my Pokemon teams for as long as I can remember. I see this as a case of being 'Old Reliable' rather than neccessarily being one of my favorites.

Gen II
Heracross - Once I found a shiny Heracross, it became one of my go-to Pokemon in HeartGold (still the second most used Pokemon on my team)
Unown - For battling, I don't think there's any denying that Unown are downright terrible. But for some reason, I've always found all of them very interesting, and to this day I'm still not so sure why I like them.

Gen III
Aggron line - Aron was the first Steel type that I can actually remember using, and it came up big for me many a time while playing on Sapphire. Now any time I go back and replay the game, I have to have an Aggron on my team.
Rayquaza - Probably my favorite legendary. I really like the design of it (especially it's shiny sprite), and it's one of the few legendary Pokemon I can actually remember using in my party.

Gen IV
Empoleon line - The Water/Steel typing of Empoleon has to be one of my favorites I've ever used. I don't normally use starter Pokemon all that often, but this was one of those exceptions.
Froslass line - While it's pre-evolution came from Gen III, Froslass was my favorite Gen IV Pokemon, again with another unique typing of Ice/Ghost. It is now one of my powerhouses on HeartGold.

Gen V
Sigilyph - I knew that right off the bat I wanted a Sigilyph in my first playthrough of White, and has it ever helped me out. Even though I haven't beaten the game yet, it is the strongest of all my Pokemon, and has gotten me out of a number of tough situations.
Simisear line - I never expected to use my Simisear as much as I have, but it is another Pokemon that has gotten me out of a bunch of tough battles. While I'm sure that these two might change after I finish with the game, they have been my favorites so far.

 

[Kenshin5]

This is going to be tuff since there is few pokemon I don't like. But I will try and decide between two.

Gen I

- Blastoise always appealed to be for several reasons. I like the design with the water cannons, I like turtles especially back then when Teenage Mutation Ninja Turtles was on and I was a huge fan. Then couple that with it being the mascot of one of the games and that Gary had a Blastoise I liked it and still do a lot.

I've loved Gengar from the opening scene of the game and anime vs. Nidorino. It has always appealed to be, even with the simple design it just looks "cool" to me. Not to mention it has an excellent movepool and stats, so I always found it very useful in my playthroughs.

Gen II

- I have never really been one to gush over cute stuff but for me Ampharos is a combination between cute & fierce. I always found it appealed especially during the early portions of the game when I could make good use of it and then maintain its use which I plan to do in BW2. I have also liked its color pattern with the predominate yellow then the black stripes and the red gems.

- Tyranitar always struck me from the beginning as pure badass. Then when I found out it was based off Godzilla & Tyrannosaurs I could see why. I always thought it had one of the most interesting, unique, and complex for the time designs for the time. As well it is one of the most powerful pokemon I ever used so it has great stats as well as a movepool too be. And Sandstream is also beneficial for the most part as well.

Gen III

- Blaziken is probably one of my most favorite out of all with Ty and Gengar being right up there. I have been an absolute fan of Blaziken ever since I first saw Harrison use it in the Silver Conference even before the third generation occurred. I was like "Wow that thing kicked Charizards ass" which was kind of awesome cause all the Charizard is the best fanboys were getting annoying after two Sagas. On top of everything Blaziken is apparently so good that it is Uber with Speedboost so the first starter to be Uber pretty darn cool.

- Pretty tricky too pick a second fav after Blaziken since Third Gen is probably my fav if not my fav so I love so many of the Hoenn pokemon. But I will pick Salamence since it is my favorite Dragon type thus far. When I first saw it it seemed different type of Dragon then the rest which appealed to me. Then its diverse stats and move pool which can go from Physical to Special also interests me a lot, so I found the usability very well.

Gen IV

- I love Gallade typing, I always thought Medicham was a poormans version to Gallade. I love the slender and sleek design too it not to mention I liked the Psychical movepool it provided as opposed to its female counterpart.

- I am putting Electivire only because it was apart of Gary, Paul, and Volkner teams. Like with Gen III I am a fan of Gen IV Sinnoh pokes. Magmotar also owned by Paul was very closed behind and a counterpart to Electivire so I like both of them pretty equally. Then Empoleon was a super awesome pokemon on top of being a starter. I love its typing, movepool the tms attached to it, overall it was just a great pokemon from start to finish. I always thought its Emperor Penguin design was amazing as well.

Gen V

- Much like Salamence Haxorus as well as the other Gen V dragons struck me as different but unique. Ever since I saw then pre-release scans I loved Haxorus. It is a great pokemon and the star of my runs in BW, so obviously for me it is quite useable.

- I fell in love with the design upon the first time seeing in when the sprites were ripped the day of the game release. Bisharp instantly caught my eye and I liked it then and still like it now.

 

[TheLeetCasualGamer]

Hard to pick

First gen: Lapras definitely- one of my favorite water types and it has the design of the loch ness monster. Which I'm always a sucker for the dinosaur look ^^
Tough for me to pick between Cubone evo line and Sandshrew evo line- I love moles and I kind of do wish they gave Sandslash more moves, but I absolutly adore it's design, I know it's more of a mouse, but I always think of it as a mole xP. But Cubone is much more reliable and still has a great design.

Second gen-
Ho Oh- it's quite possibly close to one of my favorite legendaries. While playing my HeartGold game, it just feels that it fits the setting so well. The concept of a Pheonix felt like it was tackled perfectly. It was also one of the first Pokemon Ash ever saw in such a memorable scene. ;_;
For the sake of not adding another legendary, I'd say Slowking- Anyone who saw the second movie knows it's undeniably awesome xD

Third gen-
Sceptile- I had to include this one. Brought out Leaf blade to us grass types fans. Makes the ultimate frustration reliever to a certain psychic type duo we all probably all hate to fight. The design of it is simply incredible. And though I haven't watched Ash's adventures in Hoenn, I've always been interested in his Sceptile.
Probably Absol- Very cool mythological cat with a sickle on it's head, nuff said. B)

Fourth gen-
Leafeon- my favorite Eeveelution, has move-pool that overall works well with it's stats. And it has to be the most adorable thing I've ever seen :3
Shaymin- I love the concept of different Pokemon forms and I thought that Shaymin tackled it the best next to Giratina. The concept of it being a bouquet of flowers was really cool to me and it's sky form is just awesome.

Fifth gen-
Snivy evo line- It's a freaking snake, that's all that needs to be said. I also like having the idea of good speed and an amount of utilities it can use. It also to me introduced Snake Pokemon to the move Coil which is now available for the other two snake Pokemon which is awesome
Excadrill- YES! You finally got the mole right Gamefreak! 8DDDDDDD This thing is just freaking awesome! It's design, the role in the anime, it's moves, it's stats, just everything about it!