I just tried out the Open Source PCb package Fritzing. (
http://fritzing.org/welcome/ ).
It is for basic 2 layer PCB's, but for what it is, it looks pretty good.
It has 3 view - the Schematic, the PCB and the Prototyping board layout. All three live update if you edit any of the other views. The breadboard allows for different types of breadboard such as perfboard, stripboard or the various types of plastic pluggable breadboards.
So it means you can document the prototyping, and once the prototype works, the schematic will be correct and so will the PCB. Ignore the extra blue wire on the prototyping view - I forgot to delete it after adding and removing some extra components.
Fritzing also gives the option of ordering reasonably priced prototyping directly from the package, or you can export Gerbers, PNGs, etc.
For something that takes you from prototyping to a basic 2 layer board, it is a nice package. It would take no time to learn.
Richard.