Interactive e-book by MG Ormerod, serving as an excellent introduction into the theoretical and practical details of flow cytometry.

Mr. Shapiro's “all-encompassing” standard work on almost all aspects of flow cytometry. The 4th edition was made available free of charge by Beckman-Coulter on their website for a while – it is still available in Internet Archive. It is a bit outdated, but it is still an important reference work (thanks to the pdf search function) and compendium for all questions concerning flow cytometry.

Informative website on all aspects of cytometry - with the extensive archive of the "Purdue List".
No question that has not already been asked in this forum...

A consensus paper by leading immunologists and cytometry experts covering all important aspects of planning, performing and analysing flow cytometric experiments (updated link to the 3rd edition)