Tenants in the lower income group have a hard time with these fees. However tenants who hope to rent a home with a rent of $2500 a month or more, do not consider these fees too much.

What is the right fee for Tenant screening?

what's worse. Waiting for a tenant who can pay for rent and fees or giving a tenant who can't afford fees and more than likely rent a house

I use Smart move and they charge $35 and I believe that is reasonable. I am sympathetic that someone who makes more money is better able to pay, but some things in life just have a fixed cost to them, and running credit checks is one of them. You could, if so inclined, pay the fee yourself on anything you rent out that would be considered low income.

@Jeff Gates I use Transunion MySmartMove...and I actually have no idea how much is costs because I have the applicant pay them directly.  I take myself out of the equation.

Also consider though your jurisdiction may have laws in place about how much you can charge.

I charge what it costs me with American Tenant screening - $25 for the report I choose. I don't mark it up, although it does take a few minutes of my time. I know some landlords add a little padding to the fee, but I only charge it to those potential applicants that I've basically approved anyway. The background check is the final step. 

If I can't verify their application info, or find red flags, I don't bother asking them for the screening fee. We have rentals in a lower income area, and I know those tenants cannot/will not pay a fee for every unit they apply for, and I've paid it myself on occasion.

The simple answer is - charge the applicant whatever you paid for the screening report.

The cost of a screening report can range from $15 - $45, depending on how much information you obtain. The max price allowed, as of December 2013, is $45.16 according to the Consumer Price Index. You should not charge the applicant more than your cost of the tenant screening report. 

I consider it a red flag if an applicant can't afford the screening cost. Each property is different, so your screening criteria may change between properties. Perhaps you obtain more information from prospects applying at Class A properties, therefore the screening cost will be higher. Discuss your property status and goals with your Consumer Reporting Agency to customize a report package(s) that are right for you.

I charge $30, it costs me $29.45 to run a full check.  If they pay me online, that costs me $.50 so I am making 5-50 cents.  I figure calling past landlords and what not is just part of the gig and I don't charge for my time for that.

We don't charge anything.  We get more applicants that way.

We do, however, charge $20 per person after they move in.  It's amazing how often low income people change their roommates and significant others.