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If you have uninstalled the modules, then dropping the tables should not do anything.
You should be a little careful with the IPB tables, though, as it involves core hacking to get going (was the last I heard, at least) and unless you have "un-hacked" the core, there may be some problems there.
You can perhaps just backup the tables (export the IPB tables via phpmyadmin) then drop them and if it causes problems, import the tables again.
marquee and freecontent should not give problems if you drop them.