Unfortunately this is not an htaccess issue. None of these steps seemed to help.
Well, I was busy with a shopping cart module: http://modules.processwire.com/modules/shopping-cart/
It had to be slightly altered to work with some payment service we use. For this, I added a .module file to extend functionality. This worked fine. After that I basically made a copy of that .module file, and slightly altered it (so no duplicate class/filenames or whatsoever). Thats where things went down.
Yes, debug is on. PHP: 5.3.26, MySQL: 5.5.20. Apache logs tell nothing useful. The error log is empty (apart from some 404's from a few days earlier) and the access log has nothing useful either.
We just reverted the database to the one of a week old, which seems to work. So it seems to be an issue with the modules. Still curious to know what causes this, to prevent it the next time. Or better yet, how to fix the up to date database. Reverting the database is quite a big deal, considering the work that has been done the past week.