I don't know if what you say about Microsoft's MP3 encoder is true, but it's easily avoidable by using a different encoder, such as LAME.

There is an option to set the time display. Total playlist time is certainly one of those options, but you can change it to show a variety of things. I believe it's under Settings on the main menu. I don't have my empeg in front of me right now.

Jemplode is a reimplementation of the emplode program that you use to upload mp3s to the empeg. It's written in Java, which means that it's usable by people running OSes other than Windows. It has a very similar feature set and user interface to the original.

Hijack is a replacement kernel for the empeg that has a lot of additional features for the empeg. Read more in the FAQ.