Plus many focused databases do provide methods – a great example of one is the structural biology techniques provided by The Protein Structure Initiative Structural Genomics Knowledgebase (PSI-SGKB, http://kb.psi-structuralgenomics.org), even down to the level of each step of the cloning, crystallization, what worked what didn’t for specific structures, what might work for your proteins via similarity matches and computational predictions.

A free resource you may want to add to the list is Protocols Online.

I was considering also adding the different sites where communities keep their protocols–like WormBase, or Zfin, but I generally assume the community has pointed young researchers to those.

I think some of the SciVee movies might also qualify as methods, but it is not devoted to presenting methods as many of the other mentions are.

Not really a database, but a catalog of papers with methods specific for different assays.