Turtles In Time! Man that game was sick, and had an awesome end boss, with a very unique perspective. Also, for sheer just blowing stuff up, The G.I. Joe arcade game was awesome, and very difficult.
As for my least favorite, I'd say the "Jurassic Park" arcade game. While sitting in the booth was cool, that game was way too hard for little kids with only so many quarters. And, it still is.