Canonical has produced official Ubuntu images for running on Amazon's EC2. The Starter's Guide is pretty straightforward.
The most obvious thing at first is that after starting up the instance you always need to upgrade and install packages. Eric Hammond has posted some very helpful guides [1, 2] for passing in a user script that will be run when the instance starts up (you need to join the mailing list to read them). Note that this is broken in the current AMI.
There's also a useful guide to running MySQL on Amazon's Elastic Block Store, with snapshots backed up to S3, for persistent storage.