They dont make one iota of difference unless you are running hundreds of domains and interlinking the pages - and even then unless you come up looking like a link farm you'd probably still be way below their radar - unfortunately a lot of people that dont understand SE's use this as a "fix-all" when it is really such a small issue.
Think about all the free-hosts you see listed in the top 10 - and there is bunches - where they have hundreds of sites on the same IP - and the same domain - doesnt seem to affect them
