Pick from each section
DPtHGSS
RSFRLGE
RBY
GS
Ranger games
Mystery Dugeon first two
Super Smash Bros

I can't think of anymore.

Personally I really loved the entire second generation and Emerald was also great. I'm not yet 100% sure how I feel about any of the fourth generation, and though Emerald was great, it was just too underdeveloped; the storyline was less eventful and I must say the whole item system was lost on me.

I can't say I disliked any of the mystery dungeon games either, though they still aren't on the same level as the main games.

Although I love the mainstream Pokemon games I really wasn't a huge fan of the 3rd generation. Ruby and Sapphire were alright and like Freeze said Emerald was great but was way to underdeveloped. As for Red,Blue,Green and Yellow they're just pure epicness, but with the releases of FR/LG made them even better with the exeption of the sevii islands which were totally unneeded. I personally think it would've been ten times better if they just put in the orange islands instead which would give you a few more gyms to challenge and even the orange league to go up against.
I really liked the Mystery dungeon series do to it giving you the chance to play the game on the opposite end.

I can honestly say I didn't like the ranger games too much, not because they're bad games but because I just couldn't get into them.

My is: HG, E, S, Y, Ranger:3, Sky, and Brawl.

I love the fourth generation games with the second generation games in close second. I'm not a big fan of the third generation, though. I don't really hate them, but I've never played a third generation game (Besides Blue Rescue Team, but that doesn't count here). Well, until that rumored Ruby remake for the 3DS comes out. :3

Also, I love Sky. I'm too addicted to it to try to get the TM Earthquake from the Battle Frontier in Platinum. And I finished everything there is in the game. :3

Brawl is a good game also, but I don't think it's that much of a Pokemon game. More like... A Nintendo franchise game?

I love the original G/S/C and the remakes HG/SS. Second Gen was my favorite and I've always loved the Johto region Pokemon. They have the best Pokemon and sprites. :3

I also love the mystery Dungeon games. My favorite is Sky. I'm still stuck tryin' to get the Phione Dew for Manaphy. <_<

One of my all time favorites is Fire Red. It has the nostalgia of Pokémon Blue with the fun of 3rd gen games. And it remixes the music of the 1st gen, making them incredibly awesome.

My favorite game is fire red because on their are 7 islands you can visit, it is very easy to level up your pokemon to level 100.
My team
Charizaird level 98
Hypno level 96
eletebuzz level 96
cloyster level 97
dragonite level 95
fardfetched (ch'ding) level 100 (it was traded so it over grew -_-)

Seriously? Nobody said B/W yet?

I really can't decide which I like better: HG/SS or B/W.

HG/SS - They somehow managed to take one of the best games ever and make it better.
B/W - Has the best plot of them all IMO. Well... One of the best, at least.
Platinum - Awesome plot. Team Plasma is probably the greatest evil organisation of all time.
Mystery Dungeon 2 - THIS has the best plot of them all. The graphics suck for most of the game, but Arceus the cutscenes are beautiful. I cried the first time I beat this game. Then got really depressed for a while....

My favorite Pokemon games are Fire Red because I love the remixes and the elite 4 gets stronger if you do a certain event. I was thinking about leveling up my Pokemon team to 100, but I lost interest in that.

The second Mystery Dungeon was the best of the first 2 games. The plot was better and has a lot of twists. And this is the first game that made me cry.

I like the first Pokemon Stadium because I like the battle system and the minigames.

For story wise, I think Mystery Dungeon. For fun wise, B/W

For me I enjoyed playing all the Pokemon games. I never really played Super smash bros because I really didn't like the game. Mystery dungeon series has a better story than the other pokemon games, but on the other hand, Pokemon games like fire red and leaf green provide more of a challenge for the player.

HG/SS is very closely competing with B/W for me. I think the overall alien sense of much of the old being gone, similar to what happened with R/S's release is all that's keeping B/W from becoming the indisputable top.

Ill have to go with R/S/E i dont know they were quite cool for me

It isnt on the list but BW was like out-of-this-world!

Gold and Silver, Emerald, Platinum, and Black

Mine is Pokemon Black Version and Pokemon Sapphire Version

My fave games are:

Pokemon FireRed
Pokemon Platinum
Pokemon HeartGold
Pokemon Black

I hate:
Ruby, Sapphire, Emerald, Diamond, Pearl, SoulSilver and White! (They ain't worth the moneeeeey!)
Haters Gonna Hate Potatoes Gonna Potate!

My favorites are:
White
PMD: Explorers of Sky
Soul Silver
Emerald
PMD: Red Rescue Team
Super Smash Brothers Brawl (If that counts.)

heart gold

My favorites are:

Pokemon Fire Red and Leaf Green - Not only were they simple, but they were lots of fun to pick up and play.

Pokemon Heartgold and Soulsilver - These games are a bloody masterpiece. These games top Pokemon Black and White for me any day.

Pokemon Platinum - The first two games of the three felt a little plain to me. Platinum made the Sinnoh region just so much better. The Torn World, Giratina's hood, is awesome.

By now, my favourite has to be Black/White, followed closely by Emerald.

My top 3:
1. Pokemon SoulSilver
2. Pokemon Mystery Dungeon Blue
3. Pokemon Snap