Useful papers and technical documents that everyone should read:

Nature Immunology
Volume 7 Number 7 July 2006, p681-685  "Interpreting flow cytometry data: a guide for the perplexed."
L.A. Herzenberg et al. http://www.nature.com/ni/journal/v7/n7/index.html

BD Application note
“Establishing Optimum Baseline PMT Gains to Maximize Resolution on BD Biosciences Digital Flow Cytometers”http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8389-00
or go to www.bdbiosciences.com and click on “literature”, choose “download literature”, and “view” the file
“BD Digital Flow Cytometers Application Note” (they are listed alphabetically).

“Flow Cytometry Controls, Instrument Setup, and the Determination of Positivity”, H.T. Maecker and J. Trotter, Cytometry Part A 69A:1037-1042 (2006) (You need an account for online access. There is a copy posted on the
flow bulletin board in Room 5228).

Minimum information for Flow Cytometry Data publication:
http://www.isac-net.org/content/view/606/150/

Using BD Compbeads:
http://www.bdbiosciences.com/pdfs/whitePapers/SJ-0076-00.pdf

Alternative to trypsin for adherent cells: 
http://www.cyto.purdue.edu/hmarchiv/current/0413.htm

Quality Assurance for polychromatic flow cytometry (Steve Perfetto)
http://www.nature.com/nprot/journal/v1/n3/pdf/nprot.2006.250.pdf

Purdue List Summaries:

Purdue University maintains a message board for flow cytometry, and there are several good threads that have been collected and can be found here:

http://www.cyto.purdue.edu/hmarchiv/web_summaries/index.htm   Summaries of popular flow topics
http://www.cyto.purdue.edu/hmarchiv/2006/0562.htm   Ways to minimize cell loss during washing
http://www.cyto.purdue.edu/hmarchiv/2000/0216.htm  Fixation to inactivate HIV (we ask you to use 2% fresh PFA for 2 hours). Please note the first article referenced, which shows that 1% PFA is INSUFFICIENT to fully inactivate HIV.

http://www.cyto.purdue.edu/hmarchiv/2003/0337.htm  Sorting of live human lymphocytes

Flow Cytometry Books:

www.cyto.purdue.edu/flowcyt/books/bookindx.htm
http://probes.invitrogen.com/products/flowcytometry/practicalflowcytometry.html