I use an excel spread sheet that includes price of materials per unit size, labor salary per unit time, and equipment price per unit time. Then for each item I input the size of the item, time it takes to put together and time it takes to cut, print, etc.
From that I calculate cost, but also calculate my selling price which is 2x the materials cost, plus 2x equipment cost, plus 3x labor cost. I also add 10% to the price for rejected materials, parts, etc.
The nice thing about the spread sheet is that in the end you have a price which can then be compared with prices for comparable items. At this point, if the price seems low, I can increase it a bit and know that I have a larger margin on this item. If the price seems too high I can easily see what it would take to lower costs.
To determine profit, I use Quickbooks. I enter everything I buy for my shops, including vendor fees, website cost, shop registration, transportation to pickup supplies, new equipment, materials, office supplies, etc. I input all of my etsy sales, arts/crafts/holiday show sales, wholesale sales, etc. I've got everything itemized so that I can run reports on individual items, customers, profits over a specific time period, etc. It's always nice to have a quick check on expenses vs income and of course to report income for taxes.