Generally, the oxygen transfer rate is better in a 96-square well microplate with the corners functioning as baffles [q.v. Hermann R., Lehmann M., Buechs, J., Biotech. Bioeng. (2003); Vol. 81, No. 2, pp 178-186].
Also available are new shaped wells (Flowerplate), which can further elevate the oxygen transfer. This kind of plate is only available in a 48-well format at the moment:
Microtiter plates as mini-bioreactors: miniaturization of fermentation methods
Duetz W A
Trends Microbiol. (2007); Vol.15, No. 10, pp 469-475