The MechJeb 2 manual is currently under construction!
The Ascent Guidance module can fly your rocket from the launchpad into orbit on autopilot, or can provide navball guidance to let you manually fly a good gravity turn path.
The Docking Autopilot module can automatically dock with the target ship using RCS, once you are nearby.
The Landing Guidance module lets you set targets on the ground, provides predictions for landing and aerobraking, and can auto-land at a target location.
The Maneuver Planner can be used to automatically create maneuver nodes for a variety of common orbital maneuvers.
Maneuver Node Editor
The Maneuver Node Editor provides a text interface for easily editing maneuver nodes, which is particularly useful for fine-tuning planned maneuvers.
The Rendezvous Guidance Module provides step-by-step instructions for rendezvous, and can create maneuver nodes for each step. It contains an optional autopilot function that allows fully automatic orbital rendezvous.
The SmartASS module lets you command your ship to point in a variety of useful directions.
The Spaceplane Guidance module helps you fly atmospheric craft. It can provide navball guidance for manual runway landings or do a fully automatic runway landing. It also contains an autopilot that will attempt to hold a given heading and altitude.
The Throttle Control module has useful throttle options like automatically limiting the throttle to prevent overheating, or limiting to a maximum acceleration.
The Warp Helper module lets you easily warp to certain points on your orbit.
The Custom Window system provides an editor that lets you build customized information windows.
Changing which modules MechJeb loads
It is possible to blacklist MechJeb modules, which tells MechJeb not to load them. You can use this to reduce screen clutter by modules you don't use, or to limit MechJeb's capabilities if you don't want some functions to be available.