I've been trying to wrap my head around the MKS/OKS mod which allows you to build surface bases / orbital stations which have closed or nearly closed recycling systems.  It also provides for resource extraction from the surface and construction of vessels outside of Kerbin's Space Center complex.  Some information is available on the MKS wiki, while other information is buried in the KSP forum thread.

The bare minimum for a colony is:
  • C3 (produces punch cards)
  • Kerbitat (maximum of one per base)
  • Aeroponic (maximum of one per base)
  • Inflated living space (required by Kerbitat, may need multiple)
  • Inflated greenhouse (required by Aeroponic module, may need multiple)
  • Storage space 
  • Power
For a surface colony, that is enough to support 2 kerbals.  For an orbital colony, it will support up to 10 kerbals if you use 2x inflated greenhouses per inflated habitation ring.  You also need storage space for food/water/oxygen, waste / waste water / carbon dioxide, biomass / compost, excess machinery, and spare parts.

Note: Spare parts cannot be transferred from point A to point B without EVA'ing kerbals.  All other resources can be moved around using the stock method for moving LF/Ox fuel or monoprop fuel.  Or with mods like Ship Manifest. Spare Parts (and Machinery) get consumed over (a long) time of facilities operations.

Design Note: You never need more then one Aeroponic module and one Kerbitat module per base/station. If your food/water/oxygen production is falling behind, then you need more storage for inputs/outputs and/or more inflatables to boost production.

EPL Note: When using EPL (Extraplanetary Launchpads), you must have kerbals with a medium to low stupidity rating and at least two stars of experience along with an adequate supply of Rocket Parts.  MKS/OKS also hides a lot of the stock EPL parts and substitutes its own versions as well as changes the manufacturing chain for production of Rocket Parts.

One possible flow chart for MKS/OKS manufacturing:
http://s177.photobucket.com/user/Sir_Snoopy/media/MKSResourceFlow.png.html

One way to make 3-star kerbals is to (plan on 60-80 mission days):
  1. Orbit the Mun
  2. Land on Minmus
  3. Leave Kerbin's SoI and orbit Kerbol
  4. Land back on Kerbin and recover the kerbals
RareMetals and ExoticMinerals come from the refining module and are good sources of funds if sent back to Kerbin for recovery (~700 funds/unit?).  Chemicals and Polymers may also be suitable for returning to Kerbin for funds.

Design note: The minimum MKS/OKS base crew is enough engineers to get the Kerbitat/Aeroponics lab to 50% efficiency.  They do not have to be located specifically in a particular module, but you may wish to do so because putting the right kerbal into the module has an impact on efficiency.  Engineers are preferred over Pilots/Scientists for most modules (Engineers are best, Scientists are second-best and Pilots are worst).  Experience stars matter a lot for efficiency (2-stars is probably the minimum viable, but 1-star kerbals can work in a pinch).

Design note: Biolabs require Substrate as a working material.  So you will need to harvest or ship in Substrate in order to get useful outputs from the Biolab.

Note: The Orbital Shipyard part requires that EPL be installed - otherwise it does nothing.  This also applies to the other ship construction part, the Mobile Launchpad.

Operation note: If you are going to turn on Dampeners, only turn it on for one of your modules.  This feature can help you reduce the bouncing, but turning on multiple dampeners tends to cause bad things to happen.  The Dampener is designed to clamp the craft to the surface and disable physics for the rest of the base.  Anchors, OTOH, increase the mass of the module by 2-3 tons and help with CoM (center of mass) issues.

Design note: The heaviest modules should be at the center of the base.