Espeon is my absolute favourite Gen 2 pokemon and is my favourite Eeveelution of all (Jolteon is second and Glaceon is third for those wanting to know). They hit pretty hard and when trained right can be a real nightmare for poison, fighting, ghost, dark psychic and dragon types everywhere and can hit most things not steel type pretty hard. Plus there's its Magic Bounce ability which is just brilliant, though there is also a certain satisfaction in running one with the synchronise ability and having it hold a Lum Berry - magic bounce is better though.
Heracross is quite possibly my most favourite of Bug types. When he came along, you realised that bug types could do more than just fire a stun spore and then hope for the best. Yes, Gen 2 also introduced Scizor but the best bug type attack that thing had back then was Fury Cutter and that pales in comparison to Megahorn. Heracross was everything Pinsir wished it was - both were Bug types but only Heracross had an attack to make use of it and while both could use an array of fighting type attacks, only Heracross had the typing to back it up. Even now, years later, I still adore Heracross and I always go out of my way to try and catch one, even if I have no intention of actually using it on my team.
Gligar was a pokemon that I never really had much time for in Gens 2 and 3 - it was weak and had terrible attacks. Then Gen 4 comes around. Not only does Gligar finally get an array of half decent attacks it also gets an evolution in Gliscor - probably my favourite of the multitude of cross-gen evolutions to come out in Gen 4. And how can you adore Gliscor without gaining some kind of a soft spot for Gligar?
The same goes for Togepi and Togetic. For a pokemon built up so much prior to its release thanks to the anime, Togepi was a pretty pathetic creature in Gen 2, and it didn't get much better once it evolved into Togetic. Gen 3 helped a bit by introducing some attacks that Togetic could take advantage of, such as the never-miss Aerial Ace, Shock Wave and Magical Leaf along with Water Pulse, Wish and Yawn, but it took until the introduction of Togekiss in Gen 4 to really save this line. And, like Gligar, how could I love Togekiss without liking Togepi and Togetic more than I did before?
With the starters it is very hard to choose between the three as they all have traits that I like very much. Each always had their pros and cons. Totodile was always a fun idea but it struggled to impress due to it being a physical attacker before the physical/special split of Gen 4, meaning that its Bite did less and it didn't have a water type attack to back up its typing. It also had to wait a until level 13 to get its first STAB move in Water Gun while Chikorita got the harder hitting Razor Leaf at level 8. Cyndaquil suffered a similar problem, having to wait until level 12 to get Ember. It also took a very long time to learn Flame Wheel and Flamethrower amd in general lacked versatility. Of course all that has changed with later Generations and I like all three Johto starters almost the same, though Cyndaquil I like a bit more - I used it more often than the others because grass and water types were so much more common that fire types in game.
Other favourites include Aipom, Slowking, Larvitar, Mareep, Phanpy, Crobat, Noctowl, Misdreavus, Steelix, Houndour and Hitmontop, though, like I've mentioned before, some of them I only began to like after Gen 4 came out and did many of them massive favours.