A frequent question when deciding to buy new hardware is "How much hardware should be purchased for the task?". A good rule of thumb is "as much as you can afford", but that may not be the whole answer. You should consider the following when defining specifications.
If you cannot afford a fully loaded system, can it be expanded after purchase? If you application would work best with 2GB of RAM, but you can only afford 1GB, can the motherboard be expanded to add the extra GB later on? Purchasing a motherboard that can only accept 1GB means you will need to buy a new motherboard (at least) later on, increasing cost.
How well does the design scale? If you plan on buying racks of machines, can you add new racks later and integrate them easily with the existing system? Things like switches that can accept new blades to add functionality may save space and money in the long run, while reducing issues like cabling.
How easy is it to install, upgrade, or repair? While using desktop systems in a rack is possible and will save money, replacing or repairing the systems is harder to do. A good question to ask yourself is "What is my time worth?".