My favorites? Well, I like the vast majority of them, especially those in the Houen (sp?) region.
Of course, I have some odd ones I like for complicated reasons:
1. First and foremost, I Love Nidorina the most. "Like" is too weak a word. The reason behind this was because back in the days of Pokemon Red and Blue (about a year after the release), I noticed a handful of Pokemon that get ignored, like Omanyte and Weepinbell (keep in mind this is at the time).
Nidorina, however, seemed to be (and I believe still is) the most unloved and ignored Pokemon ever. I felt sorry for her, so I started using her and drawing her til I couldn't get enough of her.
For the record, I liked Vulpix was #1 before 'Rina.
2. Chikorita. It was the cutest of the Johto starters, but it's charm isn't what it a favorite of mine. The anime had a lot to do with it, and I just loved Ash's Chikorita's personality. It was something unexpected, as far as I knew, and it was used quite well. As a plus, she was pretty spiteful towards Pikachu, and at that time I didn't like him much (I like him/it now, though).
So from that moment on I associated Chikoritas with being emotionally attached to all the wrong things. Eventually I just came to like the Pokemon altogether and she stands out of the Johto crowd in my opinion.
3. Kirlia. Before I knew what this Pokemon was or where it came from, I saw a beautiful Japanese fan art of her (it was female). I was thinking to myself, "This is a Pokemon? This thing is beautiful!" and that's pretty much it. I anticipate getting one ever since. Keep in mind they only drew Kirlia, so I didn't even know she was part of an evolution line at the time.
However, my favoritism for her was fueled later when I found a massive website devoted to the Gardevoir line. It was full of so much content I'd thought I had died and gone to heaven, so to speak. It got me into liking the entire evolution line, but Kirlia, being the first seen, is at the top.
It also helps that Ralts/Kirlia/ and Gardevoir are very unassuming Pokemon. That is, if you didn't know they were Pokemon already, I doubt you'd know by looking at them. As I've seen on that site, they can be easily mistaken for anime characters in another series, mainly because they are sometimes drawn out of concept (hair changes, clothing, etc.).
Those are pretty much the top three. Others are:
- Wobbuffet, probably for the same reason anyone else likes him.
- Mawile, seen on the same site as the first Kirlia picture I saw, automatic "must have".
- Gulpin, for odd Japanese culture reasons.
- Vulpix, as she was my first favorite.
- Dratini, because it's cute.
- Sableye, because it's weird.
- Treecko, because he's cool.
- Nidorino, just because, I guess.
- Miltank, both strong and cute, and helps the team as well.
But I really like them all. That's all that stands though, especially since I'm in a rush.