I concur with people's recommendations of VVVVVV, To the Moon, and Puzzle Agent. Botanicula is great, although I prefer the game that preceded it (made by the same studio) Machinarium. On top of being beautiful and charming, it has one of my favorite game soundtracks ever.
It was well received at the time of released, but I rarely see And Yet It Moves mentioned anymore. Admittedly I haven't played it in a few years, but I have fond memories of it.