Minecraft/McMyAdmin
If you add permissions to MCMA that has an apostrophe in it the only way currently (14/07/2013) to remove it is to manually remove it from the file groupinfo.json and then restart MCMA.
Edit messages from Servers
The triggers are located in here:
vim /MinecraftInstallationFolder/Modern/js/McMyAdmin.js
But currently this is not possible: http://forums.phonicuk.com/default.aspx?g=posts&t=1885
Help command
In console:
/?
Licence Key Recovery
Permissions issue
One issue we have ran into is when running McMyAdmin and PermissionsEx at the same time is, if you add a user, group or permission via McMyAdmin, it writes the permissions.yml to PermissionsEx with the user but with no group in between the "" parts.
To avoid this, add users/groups/permissions via /pex in the server console or in-game. To reload do /pex reload instead of /reload
Other
If you make a group that is a 'default' group (Like the Everyone group is by default) - MCMA transparently renames it to 'default' when using PermissionsBukkit as PB requires that it's called Default for people to be a member automatically.