Gisburn,
Read up a little on pseudogenes and homologies in gene sequences. That stuff strongly points to common ancestries between different species.
Simply put: If both of us were to come up with a similar database of information that we intended to sell, and used the same sources, you'd expect it to be nearly identical. However if I sneakily put in some bogus info into mine and you then have the EXACT same bogus info, I have a strong case that you copied off of mine.
Same thing with organisms and their junk dna which has the same errors as other species. How did the one come to have it just like the other?