High vacuum systems are becoming more common and a number of semiconductor processes already operate in high vacuum. The following references are ones that I have found useful in performing vacuum system calculations.
Pfeiffer Vacuum, which manufactures vacuum pumps and other components, has a nice PDF handbook which is free to download. It covers the basics of vacuum as well as operating principles of various pumps and as well as a number of practical issues.
The Handbook of Vacuum Technology edited by Karl Jousten is a thorough reference with detailed calculations for wide variety of problems in vacuum systems.