Manual and Other Resources
A good resource for new users is the MrBayes 3.2 manual, which contains instructions for downloading and installing the program, two tutorials including a qick-start version, discussions of all the models implemented in the program, answers to some frequently asked questions, a list of the differences between versions 2 and 3 of the program, instructions for compiling and running the parallel version of the program, and tips for users who want to tweak the source code or contribute bug fixes or new functionality. In an appendix, there is a diagrammatic summary of all the models implemented in the program and most of the proposal mechanisms. You can download the manual (pdf) here.
MrBayes 3 provides extensive online help through the 'help' command. Simply type 'help' at the command prompt to get a list of the available commands. Type 'help <command>' to get help information for a specific command. For instance, 'help lset' will give you the help information for the 'lset' command, including a discussion of all the available parameters and options. The help information for a command typically also includes a summary table of the options and current settings.
You can produce a text file containing all the help information for the current version of the program by using the 'manual' command in MrBayes. If you produce this file immediately after starting the program, the text file will contain all the default settings and can be used as a command reference. If you prefer not to produce this file yourself, you can download a pdf copy here.
Remember that MrBayes is free software and that it currently has thousands of users around the world. Therefore, the authors have no possibility to provide extensive user help. Please first read the manual and the command reference carefully to make sure the problem you are having is not addressed there. If the problem you are having seems to be a bug in the program, report it as described here.