I wrote an article on my blog on this and thought it might be of interest to the guitar players here. While not definitive, I've found the order that I present in the article and in the graphics associated with the article to work in most situations with the greatest flexibility.

I've read some articles that suggest you just randomly connect things together until you find something that sounds good - I think that's disingenuous and a time waster if the guitarist is really looking to have a known arsenal of tone/sound at his finger and toe-tips.

Article:

http://worshipbandwingman.wordpress.com/2014/01/15/guitar-effects-whats-the-correct-order/

Images:
All pedals into input of amp
Using an effects loop in an amp
Using amp simulation into a PA or recording device

I'm open to critique on these - leave comments here or on the blog - the blog might be a better place for more folks to see your input and opinion.