PCB Assembly Costing Help - Software tools out there?
This will depend on a large number of factors, which can interact in interesting ways.


equipment used
size of the PCB
number of different component values (in relation to the number of feeders)
size of the run
any special processing (hand-placed components, visual checks, ...)
single sided or double sided
solder and finishing requirements


In a place where I once worked the manufacturing department couldn't give accurate estimates, they simply made a run and calculated the cost afterwards. I tried to get some hard data, but there were too many factors. In the end it didn't matter for the product we made, because the manual work of folding the shielding around a small connector print dominated the costs.