Tim Lincecum is going to have a higher pitch count than say, Chris Carpenter.
120 is standard, but it depends on things like amount of rest, how the guy is throwing, control and velocity, is the guy hitting his spots or is the ball going up in the zone?, and is the pitcher a "max effort" guy.
And as far as Skip Bertman- he has ruined his share of arms, but he also has gotten his share to the big leagues- Ben McDonald, Paul Byrd, Chad Ogea, Brian Tallet, Russ Springer, Rick Greene and Shane Youman are all guys off the top off my head. Byrd and Springer in particular have had long careers. Ogea won 18 games in 95 I believe.
Kurt Ainsworth, Lloyd Peever, Ed Yarnell, Mestepay, and Brett Laxton are some of the guys that he "ruined", although I thought that Laxton was kind of overrated. And while those guys may have been ruined, they at least were drafted pretty high to where they at least got some money out of it.
Garrido and Bertman are hardly the only coaches to extend pitchers to win championships in college.