What is the best method to create seamless patterns that can be accepted on most microstock agencies?

try with adobe illustrator tool:
http://vector.tutsplus.com/tutorials/tools-tips/quick-tip-how-to-create-a-seamless-pattern-in-adobe-illustrator-cs6/

is it better to create a clipping mask for overlapping elements or to use crop command and cut away everything outside the artboard? Which method has the biggest acceptance ratio?

Maybe you can try this plugin for illustratior.
http://www.artlandia.com/

The problem (that I have) is not to create a pattern in Illustrator, it is very easy and work very well.
The problem (that I have) is how to export a tile in an usable external format for the web, stocks, etc...

Quote from: Beppe Grillo on November 21, 2013, 16:30
The problem (that I have) is not to create a pattern in Illustrator, it is very easy and work very well.
The problem (that I have) is how to export a tile in an usable external format for the web, stocks, etc...

Here is a good explained tutorial about creating a tile seamless pattern http://vectips.com/tutorials/create-a-trendy-seamless-type-pattern. The pattern on the artboard must pe included also in the swatches panel. Try then to submit to istock as they are very laborious in checking the file technically. If they approve your file then your on the right path.