If your Google Search just yielded this result I hope it will be useful. I had an Internal Server Error on only *one* of my WordPress Multisites (3.9.1) and went through the standard debugging process – .htaccess, switching off plugins, resetting theme, error logs – to no avail.
I have no caching plugin installed because it’s still kind of a development site.
But…
My hoster (strato) uses a PHP code caching mechanism called PHP Boost. Switching it off in their configuration dashboard solved the problem instantly.