Square did a good job of remaking Tomb Raider, True Crime, and Deus Ex.
I wouldn't consider Deus Ex: Human Revolution a reboot.
Yeah, Human Revolution's a prequel that leads into the first game. For that matter, Rayman Origins isn't a reboot either - It was originally intended to be at one point, but it's a normal sequel that goes back to its 2D Platforming Roots, it takes place in the same timeline as the other games. Same goes for Ninja Gaiden - It's a prequel series to the NES games and takes place in the same continuity, a bit like how Metroid Prime fits into the timeline of Metroid.
Shinobi Ninja Gaiden Twisted Metal Rayman Origins Fallout 3(this is a reboot imo, different studio and totally different gameplay. honestly don't know why they called it 3) XCOM:Enemy Unkown Super Mario 64(i would consider this a reboot...)