Bukkit

Wither skeletons are not dropping skulls when killed by a tamed wolf. According to http://minecraft.gamepedia.com/Wither_Skeleton being killed by a tamed wolf should be the same as being killed by a player. Confirmed by removing PlayerHeads plugin and seeing that skulls are dropped.

I have mobpkonly set to true.
PlayerHeads version 3.9
CraftBukkit version 1.8

If you would be willing to use vanilla drop rates for wither skeleton, in builds 3.11 and higher you can set this mob's (the wither skeleton) drop rate to a negative value to disable modified behavior, but I recognize the drop behavior is not the same as vanilla in this instance.

Since you can restore vanilla behavior with a configuration change, instead of closing this I am going to change it to an enhancement request that mobs use vanilla drop behavior for modded heads also.

This feature has been selected to be added in 5.0 alpha 3 (pending approval).  changelog here.

Keep in mind this version may still need tweaks or fixes as it is still an alpha version. If anyone finds any issues, please do report them to the issue tracker.