Visit this website for details on many on the common bugs with the minecraft beta release:

http://getsatisfaction.com/mojang

The most 'popular' bugs are listed on the homepage with the red highlighted header.

For a more detailed list of bugs visit this page:

http://getsatisfaction.com/mojang/problems/common

The server bugs we have personally noticed the most are:

1. The server software leaks memory: To combat this it is recomended you reboot your minecraft server every 24 hours.
2. Huge chunks of the world are missing: We find logging out and re-logging fixes this.