EDIT: This answer is partially outdated, the rules is now 90 days, not 3 months. The EU commission provides a calculator (albeit with a legal disclaimer) and you will find it uses calendar days, not hours.
As far as I can tell, what counts are the dates on the entry and exit stamps, which is also much easier to track and understand. Incidentally, I believe the rule is “three months”, not 90 days. I don't know if anybody tested these details in court and I would not volunteer to do it myself.
Relevant documents if you care to research this further: EU visa code and Handbook for the processing of visa applications and the modification of issued visas (both can be obtained from the EU's website).