I personally prefer using GroupManager. Since that allows me to control the different groups of traffic that comes in and out of my server. It allows me to control what permissions they actually do have. The plugin has 4 default groups. Admin (top tier), Moderator, Builder, and then Default (default tier). And obviously the owner of the server is in fact the owner of the plugin. For example on my server, the default group has access to these commands:
- help
- home
- kill
- kit
- kits.tools
- list
- mail
- me
- motd
- msg
- ping
- r
- rules
- sethome
- spawn
- tp
- tpaccept
- tpahere
- tpdeny
- warp
- warp.list
- world