For me, its mostly appearance and type. I absolutely adore Ice and Ghost types, because they have the best designs, in my opinion. Its a definite plus if the Pokemon also have a nice shiny colouring as well, and not something that makes me want to take a blunt spoon to my eyes. Some Pokemon I like just because of their shiny colouring - Piplup, Ditto, Totodile etc (I have a huge weakness for blue shinies)
There are some Pokemon I like as a result of past experiences I've had with them, though. I used to despise Breloom because of how ugly I find it, then I discovered how fun it was to use one when playing competetively online. I absolutely love it to pieces now. Although I have a love-hate relationship with other irritating Pokemon like that and whilst I like using Starmie, I will always despise it, mostly because of the misery it put me through in the 1st gen games when I was a kid and insisted on picking Charmander and training it almost exclusively. xD
A lot of the 1st generation Pokemon I like are because of their appearances in the anime, as well. I've always thought Gengar was awesome, and Onix had a huge impact on me when I first saw it. I mean, amongst all these tiny, cute Pokemon, you've got a GIANT ROCK SNAKE. It was the first intimidating Pokemon I saw, and its stuck with me. Moltres is one of my all-time favourites as well, just because the design is so...cool. Plus James' whole Flaming Moltres episode. That is probably my favourite episode ever. When I was younger I just picked my favourites based on what looked cool to me and what didn't. I'm looking for other things now that I'm older, but my old favourites still stay with me.
Kricketune is the only Pokemon I like due to its in-game cry. It sounds like some sort of freaky Amazones...thing. I've never liked Pokemon cries that much.
Really, I decide whether I like Pokemon on a case-by-case basis, although there are a few common factors I keep an eye out for~