I'm going to play devil's advocate here and say that a bad recording's a bad recording. You can compress it, equalize it, dress it up with fancy filters, but there's only so much you can do- it's always going to be a bad recording unless you're Nigel Godrich and have an analog UREI compressor to run it through.
If you really need a software for it: it's not free (yes, I read the post) but Izotope RX 11 has a great de-click function and it really isn't hard to find for free download. You could also try to EQ the clicks out.