Flojo is the best one for analyzing flow cytometry data, but it is paid one. If you don't have Flojo then you can use Flowing software of Tukru University, which is free one.
FlowJo offers a 30 day free trial, if you haven't already tried it. The trial has full functionality, so it's a nice way to make graphs if you're in the final stages of data analysis. Beckmann Coulter also offers a 30 day free trial of their Kaluza analysis software.
For free programs, we have used Flowing Software and Cyflogic.
Also, there is WinMDI for Windows plataform. However, it only reads FCS 2.0 compliant files, so it would be useful for non-digital cytometers. Alternatively, you can visit http://cyto.purdue.edu/flowcyt/software.htm This website contains a list of free software for flow cytometric analysis, including WinMDI. However some of these softwares are not updated.