The main thing is making sure you have installs for all your applications in 64-bit. Most installers are only for 32-bit and will not work on a 64-bit machine. Just making sure you can install all the programs you need is the first step. The second would be checking the vendors website or contacting their support to make sure all these applications function normally in a 64-bit environment. Also you are going to need to make sure you have drivers for all the hardware attached in 64-bit as well. Along with all these checks you also should check if everything works on server 08 as well from 03 to make sure their is no compatibility issues there either. But seems like the main thing is checking SQL 2005 Compatibility with 64-bit OS and Server 2008 they may need to send you a 64-bit installer but otherwise it should work the same.