from a recent major website re-programming / redesign (now 11 months in development now) i would say the following:
1: don't mix business and pleasure; i know the client personally (my wife works for them) so it gets sticky at times
2: make sure the contract properly outlines the work that needs to be done in DETAIL - and don't deviate from it without changing the contract
3: watch out for feature creep - this ties into 1 and 2. they will ask for more. Minor changes aside (color, text size, etc...) is ok; major changes (adding a wholesale section) is NOT ok
4: stick to your deadlines; at one point, they wanted a person in house to design the website. I said ok and stopped programming until she was done with the designs. I've had nothing but problems ever since. designs have been late; they've given me the design only to turn around and make more changes to them. SAY NO TO THIS unless the contract is revised and everyone agree's on new deadlines.
5: make sure what you need up front, you get. I always ask for 50% down. I got this, but as deadlines were broken, I never got 50% of the remainder at each additional stage. As a freelancer, this hurts.
6: Contracts usually don't take into account time you need to figure things out. One of the things I needed to figure out was how to store a file on a CDN with a link expiration so that even if someone viewed the source of the website, the files I was linking to would be invalid after 2 seconds (the best security i could offer and it was accepted by the client). But, it took 1 week to figure out how to do that even with talking directly to support staff at Rackspace. 1 week doesn't sound like a lot over 11 months, but its a lot when every week that passes is another week you don't get paid.
these are my personal views obviously and not all my freelance work goes this way. This was the biggest project I ever took on by myself and it ended up requiring a lot of engineering. Thank god, it's almost done but it was for sure a learning experience.