I don't know Popmod either and thought to have a look at it also for my own interest.
I see that it relies on access to MS Windows (which you probably have) and MS Excel (which you may also have but which I would not categorize as 'free')
A lot of cost-effectiveness modeling is done directly in Excel. If you don't have Excel you can use a free spreadsheet package, e.g. from OpenOffice.
I also get the impression that Popmod does not deal with infectious diseases. Does your evaluation need to include transmission among people?
I am also interested in a free tool to perform cost-effectiveness analysis. Specifically, I would need a software to plot the acceptability curve. Does anyone know a spreadsheet software or program that I could use?