Refresh Database; Missing Tracks; slow to skip

MSC is Mass Storage Class.  If you connect your e200 in this mode, your player will be recognized as a flashdrive. 
Transfering songs is easy, you just have to copy it to the removable drive and voila! you can now listen to it on your mp3 player.
A Disadvantage is sometimes after transfering, the player freezes on the ‘refreshing  database’ screen. Formatting the player will resolve the issue but its a hassle to transfer the songs all over.

MTP is Media Transfer Protocol.  A modified version of PTP or Picture Transfer Protocol which some cameras use.
MTP enable the e200 to play subscription music like Rhapsody.  Based on what I have read on this and other forums, most people hate this mode.
Some even tried to force MTP only players, like the express, to be recognized as MSC device.
If your not using subscription subscription music, one advantage you can get from this mode is that after transferring music, the player doesn’t refresh its database. Windows Media Player creates the database for the player.  What database?  The WMP(in MTP) or the e200(in MSC) creates a list/database of the songs so you can play them according to your preference whether its according artist, album, songs, genre etc.

You can still use MTP without using Windows Media Player. The current version of WinAmp now supports MTP.