Sadly there is no way of making any changes to transcoding - it's either on or off on a Pogoplug right now.

That said, you can make the process faster by doing the following:
Go the Media Settings page and set transcoding to "Never"
Attach the drive with your movies to your laptop/desktop
Using an application like handbrake, and transcode those videos yourself to h.264 (m4v works well)
Reattach that drive to your Pogoplug - now all our clients will recognize and play those files, but you won't need the little CPU in your Pogoplug to churn away.

you might want to play with the quality settings in handbrake a bit to make get the right balance of quality / streaming ability (depends on how much bandwidth you have), but a lot of folks have implemented this method and been pleased - hope that helps!