It's good to ask for a pre-qualification, since generally that doesn't require much effort on your part or expense on the lender's part. Be careful: some lender say pre-approval when they actually mean pre-qualification. If you haven't surrendered your tax returns, W-2s, and signed lots of papers, you're not pre-approved. It's a common problem that some lenders use the term loosely.
If you're pre-qualified, you can compare the bottom lines among competing lenders. Honestly, do not worry about fees - that's a distraction. You should look at two things:
monthly payment for principal and interest (plus MI if any), and
cash required to close (but without any assumptions of seller credits).
All the other numbers are just noise to confuse you.
The industry was forced to go to GFE 2010, but it is not all that helpful for comparing. Assumptions about taxes and insurance can change the monthly payment estimate, but you're on the hook for actuals, not their estimate.
Some lenders also assume you're getting seller paid expenses or something else. You have to compare apples to apples. And if you're worried about how much money the bank or the broker is making on the deal, you're not looking for the best deal for you.