Starting with MySQL release 8.0.0, the source code is now commented using the Doxygen documentation generation tool.

This project is long overdue … it has been a very well-worn issue, or an ever recurring wish, for the last 10 years.

Well, not any more.

The results are available at the following location:
http://dev.mysql.com/doc/dev/mysql-server/latest/

Of all the content available, my personal preference (yes, I am biased) is for the performance schema documentation:
http://dev.mysql.com/doc/dev/mysql-server/latest/PAGE_PFS.html

For those who enjoy UML notations (a picture is worth a thousand words), the documentation includes some hand written diagrams:
http://dev.mysql.com/doc/dev/mysql-server/latest/PAGE_PFS_NEW_TABLE.html

Enjoy browsing !

Edit Oct 2019:
Updated URLs to point to the latest release.
Archived doc is available here:
https://dev.mysql.com/doc/index-archive.html