xserve was discontinued in 2010? So obviously RAM manufactured for the more recent mac pro product line will perform better. The clock speed is almost twice as high!
As far as WebDirect + FileMaker, you want:
1) Fast Network - this is the most important thing for WebDirect as it is the main bottleneck for self-hosting.
2) Fast Drives - In general for FileMaker, fast drives optimized for read/write actions, SSDs are cheap now.
3) Fast RAM - RAM is also cheap, go for the max that you can fit in your system with a high performance bus speed. Most systems you can self-upgrade the ram and figure out what is the best compatibility from a place like crucial.com
4) Fast processor - multi core processors will help handle the throughput efficiently from all of the above. Xeon quad cores are usually the preferred chip for medium duty servers these days.
The number of users you expect for WebDirect drastically changes the recommendations. Also, if you have the opportunity for it, windows servers are more suited for server tasks these days as apple has really not been in the hardware space for a while.
Define "a great deal" - speed is always good no matter where you can get it. It will allow the machine to process faster. Whether you will see an impact depends on where the performance bottleneck is. If the machine is constrained for disk i/o speed then adding faster processors or faster memory is not going to help.