I thought I'd shoot up what our current stack is. I'm always interested to hear what others are working with so here's me.
Development OS: Ubuntu, Mac OS, Windows. We're 100% agnostic as long as you can use Java6.
Deployment OS: CentOS. Has better management capabilities.
Servlet Container: Tomcat. We also do some development in Jetty because it's so easy to use with Maven but we have run into a couple. We can't assume anything that works in Jetty will work in Tomcat and vice-versa.
Database: MySQL. Incredibly easy to develop with, light weight. It has held up great in production.
Persistence: iBatis. Happy with the iBatis choice. It's easy to add new queries and tweak the SQL. It's a great tool, gets out of your way.
Dependency Injection: We're big Spring fans.
MVC framework: Struts2. I'd like to see more progress and adoption in that project but we're still happy with the decision.