Do not accept a mortgage which includes a prepayment penalty.
Argue for an hour to get the documentation fee waived. That will be a good hour pay for you and if you stick to it the mortgage representative will probably relent. That fee is just a money grab, and should be illegal!
You can request an ‘assumption clause’ which permits someone wishing to buy the property from you, should you wish to sell, to assume the balance of your mortgage with the exact terms that you have. You would be on the hook if the new owner screwed up within two years. The only chance of getting this would probably be with a local institution which will hold your loan in its portfolio, and not resell it.
A new rip-off is trying to charge you a monthly fee if you pay by mail. Tick the mortgage closer off by using a black marker to black out this rip off. Watch him squirm. He will respect you for it.

Also make sure the rate is fixed and make sure that it is not a negative amortization loan. Negative loans have a monthly payment less than the interest accrued that month, so each month your loan balance goes up even though you made a payment. These are VERY dangerous and with the stagnate market, they will lead to foreclosure.

Another big one to watch out for is prepayment penalties. Some loans charge a big fee if you pay it off early. This means that if you find a better rate 2 years from now and you want to refinance, you’ll pay a big fee, which could be thousands of dollars.

Also, find out how much of a down payment you have to have, and find out if you will have to pay PMI (Private Mortgage Insurance). If you do pay PMI, find out exactly how much it will cost, and be very very clear about the terms and at what point you will no longer need it.

Get a good Realtor that you can trust. Don’t be afraid to ask them questions about your loan. Although they deal with the real estate side, not the financial side, they should be quite knowledgeable about the different aspects of the mortage process.

No early repayment penalties
No extra fees such as points
Understand P.M.I. and whether you must pay it and why
Fixed rate
repayment schedule options
lender reputation

A fixed rate, no early repayment penalties, and look for a company that won’t sell the mortgage right after settlement.

Watch the discount points, a fee you pay up front. Each point is 1% of the amount of the loan.

Fixed vs adjustable. 30 year fixed are at historical lows. Rates have nowhere to go but up so 30 year fixed is the only way to go.

Make sure you “lock in” your rate. That means the lender guarantees the interest rate of your loan until you close. This prevents you from a bad surprise if interest rates go up between now and when you close.

The biggest issue for me is a good mortgage broker. A mortgage company’s job is to find the best loan for you. They represent many lenders and types of loans. A good agent with a good rapport with you is like money in the bank. Shopping around will get you the best broker and the best deal.