From the Pokemon introduced in third generation, there are many that I like. I can't pick a single favorite. Instead, I'll list the 8 I like the most.
Slaking. Awesome design and great stats... but plauged with a terrible ability. Doesn't matter though, because it is still awesome. It helped me a lot in the Battle Frontier, destroying nearly all opposition, it was also on my team when I got at least 2 of my Gold Symbols.
Mawile. Another great design. Used it while playing through Sapphire and loved it. Then I didn't use it again until recently in Y where I learned to appericiate it even more, its new Fairy-typing and Mega Evolution being the main reasons for that.
Manectric. One of my favorite Electric-types. I have used it many times and it has always been awesome. Its movepool might have been lacking a little in the generation it was introduced in, but it gradually got better even if might not be the best. But that doesn't matter, I like it anyway. And in 6th generation, it got an awesome Mega Evolution as well.
Skitty. I like cats. Especially if they are cute. And Skitty is one of the cutest Pokemon ever, it has been an instant favorite of mine ever since I first saw it. I haven't really used it that much, though.
Claydol. Has a cool design, unique type combination, and is overall just awesome. Didn't start liking it until around 5th generation though, not sure why but it doesn't matter.
Cradily. I have a weird relation to this as I kind of love it and not at the same time. I have had some painful battles against it in various battle facilities in different generations, but have only had moderate success with it myself. Yet it has a great design and unique typing and I have started to like it more lately, so it is now one of my favorites.
Walrein. Another one I like. I kind of have a similar relation to this as to Cradily because it has been terrifying to face in battle facilitites, but I don't really feel the same way about Walrein for some reason. Have used it on some teams and it was fun, plus I like its design and walruses in general.
Latias. My favorite legendary from this generation, and one of my all-time favorites. Used to be my absolute favorite from all generations, but I can't bring myself to pick just have one favorite Pokemon anymore so now it's just one of many. I love it because I find it super-cute, it has a great design and has been useful in battle too. Have used it many times with great success for most of them.