When I practice runs for warmups etc, I use the most difficult and awkward fingering I can (a little tip from Rusty Cooley). eg 1-3-4 finger over 5-7-9 or 1-7-10 frets.

When it comes to playing it "for real" though, it all depends on what is most comfortable. That all depends on:

1) The fingering of the previous notes and the best economy of movement to get to the next shape...

2) The next shape and the economy of movement it will take to get there from the current fingering...

3) ...most of all, whatever fingering allows you to play accurately and cleanly... at warpspeed!! ;-)