A few months back we developed a little more methodology to build our pricing on projects. Maybe I was a little late to the party, but nonetheless...
At the bottom of this post are two files, one in Excel and one in Numbers, that itemize as many things as I could think of that are involved in a new web development project. We've got one (much more complex) that is always evolving for production projects as well.
Basically, it's broken into three columns on the top half, where hours can be applied for each task (some may end up being 0 on certain projects). Those hours are then talied and multiplied by the hourly rate. There's also a number of slots to insert prices for incidentals like stock photos, type faces, SSL certificates, etc. Finally, it has a calculation for buffer and discount rates.
Every cell on the sheet that has a light gray background is a formula based number. They will dynamically update as all of the other figures are entered. The Excel version also nicely uploads to Google Docs and holds formatting and formulas. Hope it's useful for you!