Yep, you can convert Quicktime (.movs) using TMPGEnc but yuo need to obtain a plugin. If you punch in 'QTReader.vfp' into a search engine you should find it. The file is only 80KB!
However, if you are not a regular user of TMPGEnc you should be aware that if you don't deselect the plugin's priority setting after use. The program can interfere with other video encoding software on your PC!