I am running MODx successfully on MySQL 5.0.51a with a slight fix to the TreeView. As Ryan said, Wayfinder and Ditto will return weirdly-sorted results unless they’re changed in the same way.
The basic rule with this MySQL version is (from my own experience) is: don’t use GROUP BY with ORDER BY.
I wouldn’t recommend the MODx team to fix these issues as a) it’s not MODx that’s at fault and b) the bug is supposedly fixed in MySQL 5.0.52 whenever it’s released.
If you know SQL well you can easily workaround the GROUP/ORDER BY bug by doing the grouping as a subquery, and order’ing the outer query instead of doing it all in one query.
http://bugs.mysql.com/bug.php?id=32202