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.
The text Vacuum Technology by Roth is a classic text, although I sometimes find the constants difficult to use because of his preferred system of units and giving values only based on air. More general formulas would often be useful.
Roth’s text on vacuum sealing, Vacuum Sealing Techniques, is also a good reference as leak management is always a consideration in high vacuum systems.
Another reference that is free to download is the conference proceedings from CERN Accelerator School: Vacuum Technology held in 1999 and edited by S. Turner.
The manual for the software package VacTran has easy to follow details for calculations of conductances and pump down time, and it is free to download in pdf format.