Protocols

DNA extraction
CHAOS DNA extraction [pdf] This protocol is adapted from Hiro Fukami. This DNA extraction method produces by far the best coral DNA we have ever seen. Simply put, it cannot be beat. Even better, you can store your samples in the DNA buffer for long periods of time, which helps when you are doing fieldwork in the tropics and freezers are not reliable or readily available. Amplifies coral and bacteria but is not good for zooxanthellae DNA... our data suggests that it can be used to rid your coral data of zooxanthellae contamination.
Quick CHAOS [pdf] minus phenol/chloroform step. Good for basic PCR amplification not AFLP.
Chelex [pdf] tends to work very well for PCR on coral larvae.
CTAB [pdf]. The old standard for snotty marine critters. The go to DNA extraction for snails and marine algae. A good second option for corals.

Miscellaneous
AFLP protocol adapted for LiCOR 4300 [pdf]
T-RFLP bacterial 16s rRNA for LiCOR 4300 [pdf]

PCR clean-ups
Sap/Exo [pdf]
MicroClean [pdf]
SpinColumns [pdf]