A Workstation for Sensitive Experiments?

etrgQUARK asks: "I am in charge of infrared spectrometers at our research center. One of the setups is used to measure the orientation of monolayers at the air/water interface, i.e. the signal we have to detect is very weak and noisy. We already have a great setup with quality components and electronics, except for one piece of hardware: the computer hooked up to acquire the data. How important is the computer in noise-sensitive data acquisition? What are your experiences? Do you have any suggestions on a workstation suitable for such tasks or is it a waste of money to use anything but the average computer system? Unfortunately, the software used is Windows-only."