After I found the cause of a specific extension interaction bug, brion pointed out that this was a common error in extensions, that is functions attached to hooks that do not return a value. Such functions previously stopped all other functions attached to the hook from running - hence the interaction issues.
Per r23133, any function that is called by a hook and does not return a value will through a full stop error. This should encourage new extension writers to use cleaner functions that avoid this, however, I noticed a lot extension functions didn't return anything. I grepped through and tried to fix them all, at least the ones on SVN, but someone else may want to doublecheck, especially for the ones one WikiMedia sites (mainly http://en.wikipedia.org/wiki/Special:Version).