Some additional things I have used:
1) Photocopying the PCB -- not really as helpful as it may seem to be, but it gives you a place to write things down and allows easy mirroring. If you don't have a program to do that, you can put oil on the paper to get the mirror image.
2) Several colored markers to trace, like VCC, GND, a particular signal. I generally get by with 3 or 4 colors (red, black, green, blue). Those colors show up well on the PCB traces.
3) At some point, I find I need to remove at least some of the components.
I have only had success with old designs. Newer designs are often based on microcontrollers.
John