Some PCB fab houses (like SeeedStudio, with their Fusion PCB service) will allow you to panelize smaller PCBs. For example, if you have a 2.5cm x 5cm board, you could panelize two of them on to a single 5mm x 5mm PCB. Or, put a 7cm x 7cm board and a bunch of 3cm x 3cm boards onto a 10cm x 10cm panel. Seeed will allow up to 5 sub-boards on a panel.
The freeware and light versions of Cadsoft Eagle limit the design area of the PCB to 10cm x 8cm. This is enough to do many projects, but when you want to try and panelize to fill a 10cm x 10 cm board, it won’t work. Plus, maintaining separate projects and updating them on the panel, and maintaining consistency of labels and reference designators can be a pain.
Panelizing PCBs for Seeed Using Eagle Free - [Link]