I believe most on the top 50 use Jupiter. I would guess most use Stratum. You could get lower bandwidth usage and perhaps slightly less rejected work with Stratum, but otherwise I think GBT should work fine. Maybe some Jupiter users can give some advice on upping the hashrate.
Does this mean that using the Bitminter client is not advisable as other clients, such as cgminer in stratum mode, would produce better results?