You could try
SickBeard, I use that along with SABnzbd and CouchPotato.
SickBeard has auto rename function built into it. If you only want to use it for the renaming function, Just click "Add Existing Shows" select the location and vola.
Make sure the folder structure is as follows:
\Show Name\Season 01\blahblah E01.mkv
If the episode is a special, then it must be in "Season 00" folder.
It grabs the details from
thetvdb so as long as it's on there, it'll grab the info.
EDIT: I just tried the following as you said you only named it by Episode number.
- Renamed an episode to E01.avi
- re-scan the folder
- made it re-name the episodes
Sure enough it renamed it to the following:
"Showname - S05E01 - Episode 1.avi"
So it should be just what your looking for.
Hope this helps.
-Mayfair