I know that changing the Windows hostname on an existing MS SQL server can cause problems if you don't update certain things within MS SQL. Are there any similar issues with changing the Windows hostname for an existing MySQL installation?
It should work without a problem. Few years ago, there were some problems with logs and replication, but those were fixed I think and even then you could easily fix that by a few parameters (pointing to the logs).
Make sure you stop your MySQL Server before the change.
Client applications are where most of the problems are... Also watch out for database links.
Also, no one can know about your specific data that may or may not use hostname, but that is something you should already know about.
Check your data where user functions are used (hostname might be parsed out to data).