Steve Vai's 10 hour workout. Which was apparently 30 hours when it was republished in one of the guitar mags 4/04. Scottgman's exercises look similar to some of the exercises in there.
Also try 1234, 2341, 3412, 4123 going up each string, then move everything up one fret on the top E and go back down, continuing the same pattern, then back up, then down one fret, then back down the strings.
Scales: 3 notes per string is good for memorization, but not the greatest for speed on the way back down. Try a 2/ 4/ 2/ 4 notes per string pattern on the way back down for better picking efficiency. There's a free online lesson about picking speed which deals with this...I just forgot where it is. Maybe over at harmony central, guitars101, or chops from HELL!!!
Pentatonic: know all 5 positions by heart. Go up and down 4 notes at a time using hammerons and pulloffs. This is somewhat useful, but I still find that it's inefficient compared to the speed you can get with chops.
And, of course, everybody's favorite: tremolo picking. Fret a pitch and pick 16th notes, then work in patterns in the minor and major scales. E.g. Hammett's solos on Kill 'em All.
Oh, and take some tips from Strongbad:
http://www.homestarrunner.com/sbemail36.html