Gerbers are text files that contain the information needed to create a PCB. I knocked up a rough and ready script to merge Gerber files to help panelize my layouts before sending them off to FusionPCB.
If the clothes iron method fails for you, try this new twist on the toner transfer process. Put a heavy hotplate on the stove and dial in a temperature of 175 °C using a thermocouple. Bond the toner image to the copper clad board by placing them print side down onto the hotplate between two sheets of paper and applying pressure with a rolling pin for 2-5 minutes. For double sided boards, flip every 30 seconds or so.