I'm impressed - I've been using Linux for years now and haven't actually braved the AMD64 version - is there really only minimal compatibility problems?
If there are particular apps then I should imagine you can build them from source to include 64-bit support.
One of the major improvements in Dapper is actualy much faster boot and shutdown times - on my new computer it actually boots faster than Win2000 which is no mean feat.
This HOWTO on the forums will probably save you a good 10 seconds for booting in the meantime however. There's a lot of cruft (included to support the maximum possible number of machines out of the box) that can simply be got rid of like EVMS.