First of all, take a good long look at MicroSoft's licenses. They have stayed in the business and gotten rich because of marketing, not innovation.
Secondly, become a LLC. It doesn't cost much, it's quick and easy, and it helps to protect you (and/or your loved ones if you die). Make sure the agreement is between the LLC and the company.
Now:
Make sure you own the intellectual property. This is critical. Some companies will try to write intellectual property agreements that would give them ownership of your knowledge of how to type.
If neccesary, give them the rights to the overall algorithm and look and feel, but make sure you don't give away the rights to code bits. You don't want other people to own your nifty specialty routines just because they were included in their code.
Write in that you will make a good faith effort to provide bug free software, but that you are held non-liable for any loss, damages, etc... See the MicroSoft licenses for the wording.
Include a clause for Force Majure (sp?). If you cannot deliver because of accident, disaster, death, etc., you will only be held liable for the return of any monies paid. If they insist on penalty clauses make sure you read them carefully. I've seen some that almost were $1 the first day, double that the second day, double that the third day, etc...
Define support. Define the method of asking for and providing support. Define the number of hours, and provide a means for them to purchase additional support.
Define the platforms you will support. You'd be surprised at how many people are still running Windows 98. I've got an antique FTIR running on Windows 98.
Get some money up front, and make sure that you tender an invoice the day you submit the final project. Require payment in 30 days in the original agreement. If it's an executable, require a temporary activation code for the first 60 days, and a final one from then on. If they don't pay, it stops working. There is no relationship (or perhaps an inverse relationship) between the size and profitability of a company and their readiness to pay.
Make sure you specify what documentation will be adequate, and then exceed that. Put some effort into making the documentation look nice. It's surprising how many companies produce decent programs but documentation that looks like a first year college project. If you are in the $10,000+ range, you might even hire a graphics artist to help pretty up the final copy (by the way, if you are in a college town students work cheap and can produce pretty good graphics design).
This is a good time to get a trip ... specify a site visit for installation and instruction. Travel costs, hotel, and per diem, OR make it all part of the contract price but make sure the price is good enough to cover it. I've gotten some nifty trips to exotic places this way. Just remember, the weather is awful in DC in August (for example).
