There is not a lot of published information on WebSphere MQ best practices. The following is a list of books / manuals and web sites that I have found on MQ best practices:
DeveloperWorks Article: The top 15 WebSphere MQ best practices
http://www.ibm.com/developerworks/websphere/library/techarticles/0807_hsieh/0807_hsieh.html?ca=drs-
DeveloperWorks Article: WebSphere MQ for iSeries Best Practices guide
http://www.ibm.com/developerworks/websphere/library/techarticles/0605_rumsey/0605_rumsey.html
Web Site: Middleware News MQ Best Practices
http://middlewarenews.blogspot.com/2009/05/mq-best-practices.html
Web Site: WMQ Best practices
http://www.gse-nordic.org/Working%20Groups/GNRC/Conferences/2007/Mainframe%20Infrastructure/ae1
SupportPac MD01: MQSeries – Standards and conventions
https://www.capitalware.com/dl/docs/MQStandards.pdf
SupportPac MD00: MQSeries – Creating design standards for applications
http://www-1.ibm.com/support/docview.wss?rs=171&uid=swg24006437&loc=en_US&cs=utf-8&lang=en
Web Site: Sebastia’s “MQ and I” Best Practices
http://usuaris.tinet.cat/sag/mq.htm#mq_best_practices
DeveloperWorks Article: Mission: Messaging: Embracing cultural change in the WebSphere MQ community
http://www.ibm.com/developerworks/websphere/techjournal/0809_mismes/0809_mismes.html
IBM Redbook: WebSphere MQ V6 fundamentals
http://www.redbooks.ibm.com/redbooks/pdfs/sg247128.pdf
