I used a 1.5" bar for my stir plate, and it works great in a 2 Liter flask. The trick to using a larger stir bar is that you can't mount the magnets directly on the fan...they would be too close together. Plus, I'm not a fan of mounting magnets directly on a fan anyway, because they interfere with the magnetic field needed to run the motor.
This is what I did:
I bought these magnets
http://www.truevalue.com/product/6-Piece-Neodymium-Super-Magnets/13923.uts at a True Value hardware store. They are very strong, and work a lot better than hard drive magnets.
Then I bought a 3/4" PVC pipe coupling
http://www.homedepot.com/h_d1/N-5yc1v/R-202303522/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053
and bought some 1/2" tube straps
http://www.homedepot.com/Plumbing/h_d1/N-5yc1vZbqew/R-100201267/h_d2/ProductDisplay?langId=-1&storeId=10051&catalogId=10053
The PVC coupling was the same diameter as the center hub on my 80mm fan. I glued it in place, making sure it was balanced. One of the 1/2" straps then fits into the 3/4" coupling, leaving me two perfectly spaced mounting locations for my magnets. I then glued a magnet to each pad, making sure opposite poles are up (and using the stir bar to properly space them). Finally, I stuck an additional magnet on each side for added strength.
The PVC coupling works really well in this application, because it adds space between the fan motor and your magnets....hence, less interference.
In addition, you could assemble multiple 1/2" straps with magnets at different spacing for different sized stir bars....or instead of adhering magnets directly to the straps, place your magnets on a thin, lightweight strip of something that screws on to the bracket. Then, if you need to use a bigger stir bar, you could just swap out the bracket or strip.
EDIT: sorry about the blurry pictures...phone was acting up that day. I also failed to take a picture with the magnets in place...