Actually, their jumping up and down helps, I think — assuming you're using the “idle to collect a lot of mobs, then kill them all” strategy.
In my skeleton-punching endeavors, I have found that, as best I can tell, dead bodies absorb hits. If I have mobs trapped in one spot and I hit in the same direction repeatedly, then only one or two will die, then nothing happens until the bodies vanish.
Therefore, if they are jumping, some of them will pop up while dying, allowing you to get more hits in. In fact, to further improve matters, I've widened my skeleton holding pen to 2 blocks wide so that I can alternately hit one side and then the other. (This picture shows only two skeletons because I just walked over to take it; ordinarily there would be a lot more, and some of them will constantly hop between the two open blocks.)
On the other hand, if you really want to stop them from jumping, such as if you only have one or two at a time, then here's some ideas:
- From the drop, let them wander into a water current which then moves them horizontally into your holding area under a two-block ceiling.
Place a cobweb block above their heads (currently not possible without cheating).
Place a trapdoor above their heads, and toggle it open periodically (with a redstone clock) to let new mobs in. These two ideas will interfere with the fall damage.