Programs for editing Proteus gerber files to panel PCBs
I find this surprising.  I've been using Pentalogix Viewmate for almost 20 years, and I've had no trouble panelizing test vehicles for fabrication.  I'm playing with KiCAD now, and I'd be surprised if I couldn't panelized designs on that platform also.

Here are some little circuits I panelized on Viewmate.


Start with the outline gerber for the panel and then orient the individual board gerbers, excluding the outline, to fit its place, then paste it in its place.  Move the gerber files around, not the circuit diagrams.

I always include bit maps in my zipped gerber packages so the fabricator knows what I want to do. If you speak to your fabricator, they may panelize multiple boards for you.