Hideo Kojima and chums have been re-recording certain parts of the MGS HD Collection to incorporate commands for the Vita's touch controls.
Apparently, one of the new lines given to Zero is, "If you flick the rear touch pad, you can slice the enemy's throat." Furthermore, andriasang reports that "in first person mode, you can pinch out left and right to stretch", though it's unclear as to exactly what that refers.
Brendan recently gave a big thumbs up to the package in his Metal Gear Solid HD Collection review of the Xbox 360 version, saying that "older players will enjoy the nostalgia in HD and newcomers can get in on the ground floor to a series that stills shows more innovation throughout than most modern titles you’d care to name. The extras and online elements will extend the package even further."
I've been relatively outspoken about my wish to see ports concentrate on delivering a smooth experience rather than shoehorning in every control interface under the sun, so I won't pass comment on this...
...but let's hope they're optional.