You can go side-by-side and use Group Policy to point the clients to the new server.
However, you lose the update approvals (if there are any updates you've specifically declined or not approved) and computer groups at a minimum.
Also the 'last seen' time for machines will no longer be valid so you could "lose" machines that haven't reported in a while.
I have not tried to export / import WSUS Setings from 2003 to 2008 yet; therefore if there are few declined updates, the clean install should be a clean, low-risk approach.