I have just rolled out new functionality that allows you to enter custom part prices, mark parts as purchased, and keep inventory of the parts you own.
When adding parts to your part list, you can customize the price information displayed by clicking on the arrow button next to the price.
Clicking on the custom price button pulls up the following dialog:
For each part, you can:
User inventory is a "new" feature that lets you track what parts you already own. You can view them all in a single page (similar to favorites), and can enter in purchase prices for each item. You can also view current prices, and add them to your part list directly from the inventory page. When adding from your inventory, it will automatically apply your purchase price for that part.
In addition to all of this, saved and completed builds will also retain the custom part price information. If you want to show how much you paid for your completed build instead of current prices, just edit your part list to include the custom pricing and save back into your completed build.