bz2 has resulted in corrupted unpacks here on more than one occasion, and it has done it without any outwardly visible error when the md5sum was good. I've had it skip a whole subdir tree in a kernel unpack on at least 4 occasions, and a missing file someplace on several more occasions. I don't have any such troubles when dl'ing and using the .gz version of things.
There has been at least one occasion where the .bz2 dl had a bad md5sum, again without any visible error as it was downloading, nuke it and go back and get the same file again and it was good. Again I've had no such troubles when using the .gz versions, so after a a while, I got into the habit of just gettng the .gz version and I've never had an instance of a bad md5sum that wasn't accompanied by site access problems.