Baal's mlvl is higher than Mephisto's, so yes he can drop better items, also the experience there is much better. As for runes, I'd guess he can drop better in NM too, but not 100% sure. Atleast in hell he can drop better than Meph.
Of course, you have to consider the lenght of the run. With a good map Meph can be run very quickly and can drop you a number useful items (such as a HoZ in NM). With Baal, the items are better but it may take a little longer to complete the run. It depends on your available MF characters. In Hell, Meph can not drop some of the uber new uniques while Baal can drop them all. I still do not do Baal runs in Hell (I hunt for the uber items in the Mausoleum and the Ancient tunnels) as sometimes the WSK can prove a tad dangerous with gloams and such.
I use a meteororb to do MF runs. It is almost impossible to die at the hands of Mephisto, but Baal on the other hand is far more dangerous. If I have to guess, I think that my Mephisto runs are twice as fast. What do you guys think, Baal or Mephisto?
Baal drops from higher treasure classes than meph on all difficulties, as far as I know. Baal runs also give you a lot more experience. (well, most of the XP comes from the 5 waves of minions)
Which you want to run depends on what you want. If you need XP to get into hell Baal is better. If you only need a shaftstop Meph makes more sense as typically you can do about 5-10 meph runs for one baal run.