We use a combination of JIRA and Google Docs and Spreadsheets. I looked into other tools as our JIRA installation is older than dirt and not as easy to use as the newer, fancier, drag and drop interfaces.
I looked into Manymoon, Zoho Projects, Insightly, Redmine, and Assembla. We're going to experiment with the Assembla free Stand Up tool. It's a very simple 3 field reporting interface that asks each team member 3 questions: What did you do last week? What will you do this week? What barriers are in your way?
In the end, I think I'm going to stick with JIRA, Google Docs, and the Assembla Stand Up tool, as the combination gives me everything I need.