1. Bill hourly for the analysis/design phase. This way the time you take to figure out what user's really want (a never ending problem in the life cycle of a project) is easier to deal with, and might increase the user's awareness of the importance of carefully thinking about what is necessary. Keep in mind, small/medium company's rates usually start around $50 - $60/hr so if you charge a little less (like $30 - $40), you'll give yourself an edge.
   
   
2. Once the requirements have been gathered, estimate a price for what the project will cost you to get done. Time is money, of course. Again, keeping in mind a competitive rate of $30 - $40/hr, estimate how long you think it will take, and then double it, at least. Take this number, multiply by $40/hr, sign on the dotted line, and start coding. :)
   
   
3. Bill hourly for maintenance!
   
   
4. Make some phone calls. If you're really not sure what to estimate as even a ballpark figure, don't be afraid to phone other web design/security consulting/<your specialty here> companies and pretend to be your client.

Of course, it goes without saying that you shouldn't fear intuition when it comes to how you bill the client. For example, one client I'm currently working with has good potential for leading to a fair amount more business, so I'm giving him a really good rate to produce a fairly simple but still high-quality shopping cartish site, and I didn't bill him for the analysis/design.

Our company also believes in free software, and helping the client by giving them the source code so they can work with it themselves or hire whomever they choose after that to maintain it. Try doing the same, and you'll be amazed at the competitive advantage that truly helping the client can bring. :)