I really like Totodile because I used it as my starter in Gold. The rest of its evolution line is fine as well, though I don't like Croconaw and Feraligatr quite as much because I never cared for their sprites when I first played GSC.
Although I didn't use it as my starter initially, I also grew attached to Typhlosion when I used it in Silver. In particular, I liked how I could buy the elemental punch TMs in GSC and teach my Typhlosion Thunderpunch so it could take out those pesky water types it was weak to.
A third Pokémon I loved in GSC was Quagsire. I picked up a Wooper when playing through Gold for the first time (somewhat coincidentally--I didn't start catching everything until after I beat the main part of the game, so I think it was one of only a few Pokémon I had caught up to that point), and I soon found myself with a Quagsire on my team. While Quagsire was somewhat useful in-game, its most appealing attribute was its ability to stop my friend's Ampharos (which I think only had electric attacks) when we battled. Furthermore, Quagsire's vacant expression is adorable!