Like others have said... just too many classics to choose from. It seems almost every round has had at least one amazing race from either the 125s 250s or 500s/MotoGP.
... can't say the same about car racing, though
Great races that come to mind:
Le Man (old circuit) 1988 -- Gardner, Lawson, Sarron and Schwantz in a classic fourway. Gardner had them gapped at the end, only for his bike to break down on the back straight on the last lap!
Suzuka 1989 -- Rainey and Schwantz. Some laps the lead changed at every corner.
Phillip Island 1989 and 1990 -- Classic Gardner. No wonder Lawson hated Phillip Island
Hockenheim 1991 -- More Rainey and Schwantz. Coming into the stadium on the last lap #34 just incredible!
Austria 1996(?) -- If my memory is correct, this was the first time Criville beat Doohan by pinching the win right at the end. And didn't Mick hate that! There's never been team orders (and team mates is a pretty loose term too!) at Repsol Honda--not when it was Rothmans Honda, either.
All of the others mentioned above were great too.
But picking out a favourite? Impossible!