"back in the day" Herzog Zwei on Sega Genesis was my favorite. Hard to nail it down to one, but if I must.. It was the first RTS and as such no one really knew what to make of it back then (the odd name did not do much to help their case!) I bought it on faith alone (the developer was one of the best) and was very surprised how deep and involving it was, specifically the 2p competitive. Would love to see some kind of true sequel someday, but that will never happen.
Otherwise, the game I play most nowadays is Drop7 on my iPhone (also on Android). The game "looks like nothing," in fact the aesthetic was so dull that when all my friends were getting into it I passed on it for a good year or so. I finally sat down and tried the demo for a few minutes and got totally sucked in. A year and a half later, I probably spend at least 45min a day on that beast. It's the ultimate "5 minutes to kill" game and I don't think I will ever get tired of it...