I've been looking thoroughly about each constructions, but I haven't been successful about when to use them.

Some rules of thumb I've found:

• This forum post and this one suggest publish in should be used when the place of publishing is a three-dimensional place and publish on should be used when it's a surface. This makes a bit of sense to me, but does not seem a very academical explanation; whereas there are some cases in which it would be hard to distinguish which kind of place it is.
• When the place is virtual, on is used. Example: Publish on Google Play

My particular cases are the following:

• To publish an application __ [in/on] Google Play
• To publish an application __ [in/on] a virtual market