I make my at home prototypes using the cold method of toner transfer and etch with 

hydrochloric acid and hydrogen peroxide.

Here are the steps I take.

1. Print a PDF mirror image of the top, pad and via layers in Eagle.

2. Go down to Kinko's/FedEx and have them print the image on their cheap glossy paper with the black and white printer on the highest/darkest settings.

3. Cut a copper clad board to fit circuit size.

4. Scrub the board with a tough pad (this is like a green scrub pad from hell) until it is shiny.

5. Wipe down board with alcohol.

6. Prepare two old PCBs, one on the edge of a table and the other will be clamped using a strong jaw clamp from Home Depot.

7. I lay the board on the edge of the table and using a combo of 3 parts acetone to 1 part alcohol (I'm using dollar store stuff here, 100% acetone and 50% alcohol) I wet the board thoroughly.

8. I then lay done a copy of my artwork face down and wait just a second.

9. I'll first press one finger down to hold in the place and using another I'll roll my finger down the board.  If it's bigger than my finger, I'll use a hard rounded surface to press firmly (with out mashing it, don't want to distort if).

10. Next lay the second PCB on top, clamp tightly and come back in an hour.  Most likely everything as evaporated, if not let it dry out.

11. Remove paper under running water.  I like to let the water remove the paper as much as I can.  Then I'll light run my finger over the board to remove the rest.

12. I then lightly scrub the board with a paper towel soaked in alcohol to remove any remaining bits of paper.

13. Next it outside to etch with a mixture of 3 parts H2O2 to 1 part HCl.  Takes about 8 - 10 mins unless it's cold.

14.  Clean board with acetone to remove the toner.

Using this method I think I've had one failure to transfer, and then it's just scrub it down with acetone and do it again.  I easily do .016 traces with this method.