You can goto ConsumerReports.org (have to pay to access most of their site, unfortunately, but you can get just a 1-month subscription for like $5) and get a printout of what the dealer will pay the manufacturer for the car you are considering in its absolute base trim and then what the dealer will pay for each manufacturer-installed option. If memory serves you can also get actual cost for dealer-installed options as well.
Figure out how you want the car setup then work out what it cost the dealer. Come up with whatever you think is a fair percentage of profit (be realistic - $12.37 over actual cost isn't gonna cut it) and tell 'em that's your bottom line, take it or leave it. If the first dealership won't accept it then the next one will. Or the third, or the twelth, whatever. For the 10 or 12 bux you'll spend on ConsumerReports for a short membership and the printouts it can save you several thousand so it's well worth it.
Just my $0.02.