PermissionsBukkit uses the command /permissions, with aliases /perms and /perm. All commands have in-game help and are usable from the server console.
/permissions reload - reload the configuration from disk. /permissions check <node> [player] - check if a player or the sender has a permission (any plugin). /permissions info <node> - prints information on a specific permission. /permissions dump [player] [page] - prints info about a player's (or the sender's) permissions. /permissions setrank <player> <group> - set a player to be in a group with per-group permissions.
/permissions group - list group-related commands. /permissions group list - list all groups. /permissions group players <group> - list players in a group. /permissions group setperm <group> <[world:]node> [true|false] - set a permission on a group. /permissions group unsetperm <group> <[world:]node> - unset a permission on a group.
/permissions player - list player-related commands. /permissions player groups <player> - list groups a player is in. /permissions player setgroup <player> <group,...> - set a player to be in only the given groups. /permissions player addgroup <player> <group> - add a player to a group. /permissions player removegroup <player> <group> - remove a player from a group. /permissions player setperm <player> <[world:]node> [true|false] - set a permission on a player. /permissions player unsetperm <player> <[world:]node> - unset a permission on a player.