I am told by the mortgage brokers we work with that we are in the minority of commercial lenders in that we require no upfront fees (the borrower pay appraisor directly). If you decide never to pay an upfront fee you still may be able to get your deal financed but you will eliminate many potential lenders who might have more favorable rates or terms.
I think that an informed decision is called for here. If the fee is reasonable, and seems like it is covering lender's expenses, AND your research on the lender shows that they are legitimate, then I would pay the fee if I had confidence in my deal and in the lender's ability or willingness to fund.
I definetely would not pay upfront fees that wind up in a mortgage broker's pocket, or that are commitment fees that represent profit to the lender rather than expense reimbursment. The exception might be some banks that do require a commitment fee - however I would seriously consider other sources before spending a significant amount of capital on upfront fees.