We're planning to build a very powerful computing machine to serve bioinformatics application here at HCFMUSP (check my profile). I know that the common choice is to build a cluster or go cloud. But our adventurous spirit urges for some experimentation. We are somewhat envious of proprietary solutions using FPGA cards like these ones:
From what I've read, FPGAs are fine, but expensive. Have you looked into other, more readily available (and easier to program, mostly) architectures? I'm thinking of GPUs (CUDA, OpenCL), and Cell B.E. chips (in Playstation 3, programmable via C/C++ and also via OpenCL)?
All depends how diverse will be the applications running on this beast. If the end users are from DNA sequencing, NMR, mass spec to crystallography and the total number o applications is say 50+ it is unlikely you will be able to support it not even on FPGAs but even with CUDAs. Either something installs / compiles (almost) out of the box or you may have to drop it. Software authors will be of no help when it comes to porting it (and possibly a bunch of libs they depend on) to a new platform they do not even have in house.
On the other hand whenever problem is restricted to one domain, FPGAs are great. I used SORCERER for protein mass spec and DeCypher for blast searches.
Anyway, have fun with new servers, whatever they will be :-)