I think Tom hit the nail on the head.
I estimated commercial projects for the past several years and the first thing I learned was to never put a bid out based on sq/ft. Just too many variables. Specs alone can kill a job. So I have always qualified my bid to death on what I was going to include and exclude.
If you are new to estimating and estimating homes you can go to a Home Depot store and pick up a free CD that carries their pricing and also has an estimating package included. I have found that the hours they show for any given task are very close to the units that I use. Since I've never bid residential until now I kind of felt like I have been getting away with something considering the cost of esimating packages.