what time of year will this be?
i would generally advise against booking a flight+hotel package at a place like the sites you mentioned, or expedia, travelocity, etc., even though doing so might save you a little money.
for something like a honeymoon i would be looking at tripadvisor.com and lonelyplanet.com and similar sites to try to find the really special, smaller hotels. (after you pick one out, you might then go back and see if you can get a flight+hotel deal somewhere).
second question is what type of travel do you have in mind? some people want beachfront relaxation for most or all of their honeymoon. is that you? if so, obviously europe doesn't make much sense.
are you looking for a relaxing stay in a small town or in the country? in the mountains? a mixture of big city and smaller town/village? only big city/cities?
europe can offer any of these things, and many places in north america, asia and australia/new zealand can too.
instead of us just randomly tossing out places, maybe you can tell us a bit more about your desires.