we are using commercial software for the gel analysis. But after that I switch to freeware for my RAPDs. I just love famd (http://www.famd.me.uk/famd.html) - it is very comprehensive and can deal with missing data. So once you get your binary character table (for instance with GelJ) you can use famd to analyse genetic diversities and construct the according dendrograms. The output is in ph-format which is easily displayed (and nicely formatted) for instance in Dendroscope (http://ab.inf.uni-tuebingen.de/software/dendroscope/welcome.html).