This tutorial was done on Windows. Authors claim it could also be used on Linux by using Mono, but I haven’t tried and don’t understand a lot about Mono to see what could be done. I am switching to Linux nowadays, so I’d be very grateful to anybody that’d make instructions on how to launch it, however – and I’m sure other fellow Linux-wielding engineers will be grateful, too =)
The tool I’m personally using to panelize boards is GerberPanelizer from ThisIsNotRocketScience.nl. It’s a wonderful tool that allows you to panelize PCBs, mainly using tabs&mousebites. There are more tools in the archive, they all seem Gerber-related but I didn’t even go through them =)
I’m using KiCad myself, so I’ll mainly work with KiCad-made gerbers. The panelizer project page has some tips for Eagle users as well, related to CAM files, so if you’re an Eagle user, check it out, it can help with some moments. I’d love to cover Gerber generation for different EDA packages (actually, not), but Internet has plenty of tutorials on those. There’s a good online Gerber files viewer (needs gerber ZIPs) which gives out pretty renderings of your board, so you can use it to check your Gerbers – I do that all the time (and KiCad 3D viewer helps, too).
No matter your EDA tool, the workflow is simple – first, you have to have gerber files in separate folders for each project.
Generate gerbers for each project that you want to include on the panel. You should have a couple of separate folders with gerber files – or in case you want to panelize multiples of the same board, just one folder.