The Active Time vs Total Time issue is the biggest source of differences, though.
Not sure about the other examples, but Warcraftlogs will do Damage/Time, while Recount does Damage/Active Time, so if you died, or had downtimes, Recount will show higher DPS for you than Warcraftlogs.Similarly to Stormlash, if you have ret paladins, Recount will give Blessing of Might damage to the recipient, while WCL gives it to the pally. Enhancement shamans have Stormlash, which Warcraftlogs shows as the Enhancements damage, while Recount will show that the one with the buff did the damage.