The first thing I've gotten in the habit of doing immediately after selecting "Flip Names" on the mirrored side is to fix the roll. I select all the bones on the original (left) side, go over to the tools panel on the left, click on options, then under Armature Options click the "X-Axis Mirror" box, then hover my cursor over the highlighted objects and press the "R" key. This automatically sets the roll the way the bones are supposed to bend. Done and Done! :)
