Hitman Absolution perhaps holds first place for amputee characters.
Thirst, there is this evil guy Travis from the Agency, who is an arm amputee and sport a very high-tech prosthesis:
The other one is Dr. Green, who is a leg amputee. Other NPCs tell a sad story about how he lost his legs with very stereotypical notion of kids who suffer grow up into psychopaths:
Talking about stereotypes: the game has a most delicious impression of female Texan accents. This is a must to hear by all Southern accent devotees:
In general, that’s a solid game and a good addition to the series canon. Give it a go.