How does popular Minecraft server admin tool McMyAdmin handle whitelists?
The Preferences tab lists the following options for Whitelist Mode: No whitelisting, Match any group, and Lockdown. And does it use whitelist.txt to set these options?
No whitelisting = Self explainatory
Match any group = Allow anyone who is assigned to a group to join
Lockdown = Allow anyone who is currently playing to continue playing but prevent any new connections.