If we're talking about the flat end of a cylinder and you simply want it to be centered, when you open the Hole dialog note that the 'Que/Status' line is asking that you "Select planar face to sketch or spcify points" so simply set the 'Snap Point' option to 'Arc Center' and select the circular edge the cylinder and it should snap to the 'Arc Center'. Now just hit OK and you're done.
John R. Baker, P.E.
Product 'Evangelist'
Product Engineering Software
Siemens PLM Software Inc.
Industry Sector
Cypress, CA