The primary ATA controller in the Rev. A is "touchy" with two HDDs, while the Rev. B is fine with them. In reflection of this, most Rev. As shipped with a single hard drive bracket, while the Bs generally shipped with the dual-stack bracket seen on towers up through the Quicksilver.
The Bs have larger heatsinks-I've favored them for G4 upgrades for this reason.
Finally, anecdotally I've found that the Rage 128 in the Rev. B generally comes with the DVD decoder board, while the Rev. A lacks this, although I don't know if this is universally true.