Bold text Edit: Kevin McHale (Artie) is the shortest (even out of the wheelchair). Kevin is 5'7" (this has been stated by him in an interview) whereas Darren Criss (Blaine) is 5'8" or 5'9", depending on where you look.
Blaine, all the way !
(Or Artie, considering he's in a wheelchair :/ )
I believe Darren Criss (as Blaine Anderson) is currently(as of Jan. 1, 2012) the shortest of the male regulars in the cast, standing at 5'7". This is the height that originally was circulated when he joined the show in early season two. His IMDb currently reads at 5'9", but reported height is sometimes shifted in the business because of image concerns. Given his age, it is unlikely he has grown during the last season. If the current listing is accurate, Kevin McHale (as Artie Abrams) would be the shortest at 5' 8".
If counting who has been the shortest male regular at any point during the series, to date the trophy would go to Chris Colfer who stood at 5'6" when the series began, but who now stands at 5'10 1/2".
I'm pretty sure its Kevin McHale, but thats just based on this picture.