One of my favorite comprehensive guides is from Jake's Bones. There's even a handy chart that tells you what methods work best for which stages of decomposition.
One of the most well-done and beautifully laid out bone-cleaning guide comes from my friend Corinne of Stuck With Pins, who is a hobby collector and does not want to maintain a dermestid beetle colony. Make sure you read the comments for additional input from Corinne and her readers.
Speaking of dermestid beetles, if you are interested in starting and maintaining a colony then the Kodiak Bones & Bugs guide is the one for you. Dermestid beetles (not domestic beetles, or dermatitis beetles. Dermestid!) are flesh-eating beetles that can also be quite finicky. They don't smell great, they work slowly, and you have to maintain a certain climate for them. When you maintain a colony you have to remember that they require care and attention - if you do not take care of them, they will die. Please be a responsible caretaker if you choose this method of cleaning bones!
The University of Arizona published a comprehensive guide on cleaning skulls to museum standards. That guide can be found here.
Shearwater also published a comprehensive guide, but theirs covers methods for cleaning the skulls of seabirds. DO NOT TOUCH A DEAD SEA BIRD UNLESS YOU HAVE A FEDERAL PERMIT. Illegally obtaining specimens contributes to poaching. Don't turn your bone-collecting hobby into one that is detrimental to the environment. This guide is specifically meant for federally-accredited educational institutions like museums and universities or federally-licensed commercial taxidermists who donate remains to museums when their projects are completed.
Lastly, Jana Miller of Bonelust has published a series of posts on her blog on her favorite methods. She lives on a large plot of land and has room for a bone cage. I do not recommend a bone cage unless you can keep it very far away from your home - they smell ripe and not in a "juicy peach" sort of way. Here are two different posts: one and two.
What are your favorite bone-cleaning guides? Are there any I left out?