I really like the setting and progression of HL1 but I feel like it didn't really get perfected until Black Mesa. Solid foundation for its sequel though.
CTR really deserves as much credit as MK in my eyes, vibrant colors and sound design, fun items, and a great cast. Should really get around to playing Nitro-Fueled sometime...
Another one of the quintessential games from my childhood. I think Spyro 3 is pretty good too, but Ripto is definitely an iconic villain for me, right up there with Dr. Nefarious.