Gen 3: I like a lot of Gen 3 Pokemon, so in trying to keep the list a reasonable size I've left a bunch out: Glalie, Cradily, Whiscash, Shiftry, Ludicolo, Mawile (+Mega), Sableye (+Mega), Slakoth, Torkoal, Mega Camerupt, Trapinch, Solrock, Walrein, Kecleon, Claydol, Shedinja.
Gen 4: On the opposite, I'm not so fond of Gen 4, I think it's the weakest generation overall with a lot of its lines, and also there's far too many legendaries. My favourites would be Gastrodon, Tangrowth, Yanmega, Roserade Mismagius, Empoleon, Toxicroak, Abomasnow, Porygon-Z.
My favorite Gen III Pokemon also happens to be my favorite one of all time. No one will ever be able to beat the awesomeness of Grovyle in my book.
My second favorite from this generation also happens to be from the same evolutionary line. It’s Treecko!
Third on my list is the awesome steel behemoth known as Aggron! How can anyone hate this bizarre combination of steel and rock? Best of all, he’s environmentally conscious too; he plants trees!
Number four is probably the cutest Pokémon ever, Skitty! I love her design and voice so much! Cats are my favorite animals anyway, so I automatically have a reason to like her.
The last Gen III Pokemon I’m going to mention on this list for now is Swampert. What happens when you take a starter who is already cute (and a popular meme), a middle stage who is slightly more menacing, and mix them together? Why, you get Swampert, of course! His design is so cool, combining the best aspects of Mudkip and Marshtomp. And the face is adorable, almost as adorable as Mudkip’s.
I can’t say I really found that many Gen IV Pokemon all that exciting, in my opinion, so this list will be kind of short.
Munchlax was an easy choice for me when I was thinking of ‘mons for this list. He’s funny, he has a cute design, and he’s a baby Snorlax. What’s not to like?
Buizel is probably one of my favorite ideas for a Pokémon. An unholy cross between a weasel and a flotation device is such a brilliant concept.
Lucario pretty much rounds out my list. Yeah, I know, the furries have kind of tarnished his reputation, but, once you look past that, you’ll find that he is an awesome Pokémon who you do not want to mess with.
Quite a lot in the 4th gen
very few in the 3rd gen
overall these two gens, Leafeon and Glaceon easily take my favorite vote, didn't need to think of it, they are the cutest, and are Eevees
for the 3rd gen - my favorite in the gen is likely Delcatty, as there where no Eeveelution or other foxes introduced in the gen - almost 90% of this gen Pokemon I don't like at all
some of my other favorites in the 3rd gen: Poochyena/Mightyena, Zangoose, Zigzagoon/Linoone, Taillow/Swellow, Aron/Lairon/Aggron
for the 4th - easily as I mention, Glaceon and Leafeon easily take my heart and vote
some other Sinnoh Pokemon I like include: the kittyz Shinx/Luxio/Luxray and Glameow/Purrbeauty, and also love Buizel/Floatzel, Stunky/Skuntank, Pachirisu, Chatot, Riolu/Lucario and of course, one of my favorite legendary too, Giratina
Gen 3: Sableye, Mawile, Sharpedo, Lunatone, Cacturne, Shedinja, Dusclops, The Regis, Surskit, Cradily, Snorunt.
Gen 4: Vespiquen, Mowtom, Tangrowth, Porygon Z, Yanmega
It's preeeeeeeeeeeeeeetty obvious what the bolding represents. Anyhow, I've always held a deep fondness for Gen 3 in particular, and it persists even to this day; Gen 4 on the other hand, while it did bless us with the Phys/Spec split, I seem to have grown increasingly sour towards most of the designs introduced there; especially since many of the designs, particularly the legendaries/mythicals and some of the new evos, were built on something of a 'bigger, fatter, cooler, and more complex' mentality, which is a type of style that I've grown more peeved towards these days.
Gen IV I have quite a few since this is my favorite gen, the ones I definitely like most though are: Piplup line, Glameow/Purugly, Weavile, Leafeon, Glaceon, Froslass, Gallade, Bidoof/Bibarel, Garchomp, Buneary/Lopunny, Porygon-Z, Lucario, and Cresselia.
For Gen 3, Medicham (more specifically Mega Medicham). I know a lot of people don't like its design, but that was never really a problem for me. It has a cool type and a fantastic ability. That's enough for me.
For Gen 4, my absolute favorite Pokemon, Porygon-Z. I've always loved the Porygon line, but Porygon-Z edges out Porygon2 because of the whole glitch thing it has going on. Then there's Adaptability and Z-Conversion...