Mechanical Calibration

First, your machine should be as smooth as it can get. Makerbot has a very good start page here.

ReplicatorG settings (v. 0016)

Machine -> Onboard Settings -> Set Extruder Parameters

Extuder thermistor

These settings depends on the type of thermistor you use. You will need an external device to measure if these settings are correct. With the default thermistor:

Beta                  4066
Thermistor Resistance 100000
Base Temperature      25

For tips on how to calculate your thermistor settings, look here.

Heated build platform thermistor

Same as above.

Reversal parameters

Time to pause (ms)                  44
Time to reverse                     88
Time to advance                    200
Min. extrusion time before reversal 44

PID parameters

P parameter 5.0
I parameter 0.09765625
D parameter 5.0

Wikipedia has an article on how PID controllers work

Tuning Skeinforge

Start with Makerbot's How to print page:

The fourth parameter has 3 separate settings:

• Carve: "Extrusion Width Over Thickness"
• Inset: "Extrusion Perimeter Width Over Thickness"
• Speed: "Extrusion Diameter Over Thickness"

All skeinforge settings can he found here.

Makerbot suggests these defaults for the v2 nozzle

Test prints

http://www.thingiverse.com/thing:2064 is a good start: it contains 3 test objects that will show most common problems.

The Makerbot Calibration page suggests these tests:

1. add raft adhesion check
2. [http://www.thingiverse.com/thing:2064 Set of Calibration Prints.
3. add tall object print test
4. add wide object print test and platform flatness test

Not complete yet :-)

See also this post on Makerblock called 

How to caliberate and tune Skeinforge for your MakerBot

Improving your extruder

Extruder lock-ups, alternative extruder designs:

http://www.reprap.org/wiki/Mendel_extruder