All the advice below is fine, and is perfectly applicable to FSBOs. But let me try taking it a step further. How about houses that not only "are not on MLS" but also that aren't FSBOs? In other words, they aren't on the market at all right now.
Maybe they were at one point, but the listing was expired or withdrawn. Or maybe the house is sitting there vacant, but not on the market. Or out-of-town owners are renting the property, but really are open to selling it. Or a couple is getting a divorce, and the property isn't yet listed on the MLS. Or someone's a payment or two beind on the mortgage, looking at the possibility of a foreclosure, but hasn't listed the property. There are a lot of ways a house might not be on the MLS but still might be purchased.
Realtors can help you in many of these cases. For instance, they have access to expired and withdrawn listings. In many cases, the owners still would like to sell; it's just that the house didn't sell. Realtors also have access to out-of-town owners. A postcard or letter mailing, or phone calls, to out-of-town owners can turn up people who'd like to sell their properties. You can also purchase compiled lists of most of these.
For divorce situations, there are compiled lists, or you can go to your local courthouse and compile the list yourself. Or, look for bad rental situations in which the owner might be sick and tired of renting, and would prefer to sell. Go to the courthouse and check the court cases for eviction proceedings. Contact the owner and tell him/her that you've got a solution to their landlording headaches; you'd like to buy the house. For vacant houses, drive around the neighborhoods your interested in. Take a pad of paper and a pen. Jot down the addresses of vacant houses. (You'll find some.) Then go online to your city or county (or township) and find out who owns the property. Call or write, offering to buy it. Or...go through your newspaper looking at houses for rent. Call the number and ask if they'd be interested in selling. (I've done that, and it works.)
Once you find someone (or someones) interested in selling, you need to know what you're doing. Some Realtors can help (though, frankly, some will be uncomfortable since they're out of their element). Private real estate investors will also help.
Hope that helps.