I have to disagree with my colleagues a little here . . .
What does that fee cover? I don't charge a fee personally, but I used to work in "big name bank" retail, and it was policy at most to charge between $295-$895, depending on the value of the house (costs more to appraise a multi-million dollar property), before so much as a preapproval would be granted. If a loan hit the system (happens when credit is pulled and application is taken) and the customer had not paid the fee, the entire fee was deducted from the loan officer's paycheck.
Additionally, I worked once at a shop that charged an application fee of about $500. That fee covered the cost of an appraisal (which was most of it, 350-475 in my area) and a credit pull and other inceidental processing costs. It was company policy that if the customer withdrew or was denied, every dollar that was NOT used to pay outside providers already, such as the appraiser and the credit report company, would be refunded to the customer. When the loan closed, any unused fee was applied directly to the closing costs. The shop had VERY low fees beyond the application fee, because the high level of commitment from borrowers kept overhead costs well below the competitors. In the end, this usually worked really well for both parties.
While it is true that that some brokers collecting that fee may be simply padding their pockets, some may be legitimately assessing your commitment to the process and trying to avoid being stuck holding the bag.
In retail banking, an application fee is standard nowadays. Every big national bank I can think of charges one at some point in the transaction (thoug it may not be until closing, if the loan officer thinks you are a good risk), and the lowest I've heard is $295.
Get a full "good faith estimate" of all costs, and a detailed explanation of exaclty where that $600 is going. It may be a scam, but it may also just be a sign of the times. Money is not flying around the mortgage world like it used to be, and some mortgage brokers and lenders have steep overhead costs and experience high fallout from borrowers who just want to apply all over town, get a few free appraisals, underwrites, and credit reports (cost to each lender about $400), and then make their decision.
If the over-all costs are lower than the competitors, the application fee should not be a turn off unless you think that for some reason you will not qualify for the loan when all is said and done.
But if the broker/lender cannot tell you EXACTLY what the application fee will be spent on . . . run, run for your life.