PermissionsBukkit - the Official Default Groups Plugin
Current Version: v2.3 (beta v2.4)
Find PermissionsBukkit on the forums!

It's been a long time coming, but with the accomplishment of build 1000 Bukkit has finally accomplished a built-in Permissions system (codenamed Superperms). For more info on how they work, and how to integrate them with your plugin, see the official Permissions FAQ. Keep in mind that you should rarely, if ever, have to hook this plugin directly; instead keep things in the realm of checking player.hasPermission("yourplugin.node"). The FAQ thread has more info on how to use Superperms with things like chat prefixes/suffixes.

Features:

Storage of users and groups in plugins/PermissionsBukkit/config.yml.
Both users and groups can be assigned individual permissions and parent groups to inherit permissions from.
Support for global and per-world permissions.
Reload configuration from file without reloading the plugin.
Ability to check if a player has a specific permission node.
Ability to dump all permissions a player has and the plugins that set them.
Ability to print plugin, description, and default for a given permission node.
Ability to modify the permissions of groups and users and the groups of a user in-game.
Built-in antibuild via the "permissions.build" node (defaults to allowing anyone to build).

Downloads:
Current Beta Version:
PermissionsBukkit v2.4 beta (details)
Current Version:
PermissionsBukkit v2.3 (jar) (details)
Previous Beta Version (for older than 1.7.6):
PermissionsBukkit v2.2 beta (details)

Other Important Information:
Commands
Configuration
FAQ

Changelog:
For changelog information, known caveats, and other release notes, see the entries on the files page.

Plugin Metrics
PermissionsBukkit gathers some information about your usage via PluginMetrics. The information is available here, and you can disable metrics on your server by changing 'opt-out' to true in plugins/PluginMetrics/config.yml. You can view your own stats with the /perm about command.
PermissionsBukkit collects this information about your specific usage:

The number of groups, users, worlds, permissions, and permission roots (first parts) in your configuration.
Whether you use per-user permissions, per-world permissions, group inheritance, and API features.
Whether anti-build is enabled, assigned to the default group, and has a message.
Whether debug mode or custom permissions (permissions.yml file) are in use.
Whether the example user "ConspiracyWizard" is in your configuration (this is not a real person).

Additionally, some information is collected by PluginMetrics by default:

Java version
Operating system
Authentication mode (online/offline)
System architecture (32/64-bit) and core count
Game version
Server location