This is the To-Do list of MencodeMe. Here I'll list things that I plan to add in the future. Please note that "in the future" does not mean next week or next version, it means that I intend to do this someday.
To-Do:

Add boxes to encode audio

Change the log name according to source

Fix VBV size

Specify audio size instead of bitrate

Add a way to start straight in the second pass, if the log exists.

Exchange crop and resize positions

Save settings

Save temp.conf and encode.bat with different names.

Change output filename

Specify input FPS according to source to avoid sync problems

Change GOP for KVCD/KSVCD
Already done for the next release:

Fix subfolders path replacing / with ./

Add the noise trick to avoid low bitrate problems
The topic is locked to keep it clean. If you want to suggest a feature, post a new thread.