I read somewhere that OEM comes along with Oracle Database, but does it require some management license and how the license is counted? is it per physical/LDOM server based or per control domain based or per processor based?
The license packs for OEM (and Grid Control) are sold by "named user plus" or by cpu. You can find the details of the price on Oracle website.
Beware, there are some minimum quantities that vary according to the metric you choose or to the license of your database.