In F1 2010 I used a manual because the lap times are better it seems. On the really technical F1 tracks it's a reference point, sometimes the only way to know if your at the right speed for the given corner is to be in the right gear.
In Gran Turismo I've used auto gears, not tried manual yet. I know in the Vettel challenge it would be almost impossible to use manual, just too fast and your at a diff speed each time you hit the same corner. With that car sometimes you can flat foot corners, the next lap your having to brake.
Now if I got into a series of the same cars that ran the same tracks, than I might consider a manual for the reference point braking and corning, and to try and shave tenths or hundreths off my lap times.