I believe the OP asked not about filling the empty space on particular PCB, but on PCB order - ie. more sub-PCBs panelized on single big PCB, where panelization process usually doesn't allow 100% utilization of space you pay for. Then, throwing a tiny breakout board here and there gives a sense.

I personally don't. I mean, I usually fill everything with ground planes where possible. Also, as @esot.eric.wazhung mentioned, you can fill the unused space on the planes with vias. This technique is actually called stitching and it is generally used in power supplies/high speed designs to increase thermal conductivity and to decrease the overall impedance of ground connections (but the spacing of the vias matters in the latter case, and depends on the frequency of the signals flowing on your PCB).

I usually do .1in spacing breadboard in all unused space... Size those holes/pads right, and you can create a "ground plane" and "power plane" on a 2-sided board. Throw in vias between each "square" of four .1in holes, and attach alternating rows of vias to alternate sides. Then every .1in pin has a power and a ground nearby. Draw a silkscreen line across each row of vias connected to that side. Can do quite a bit of SMT stuff with that, too.

(Shameless self-promo: Here's a picture, 'cause it's hard to describe:

http://hackaday.io/project/3602-audiothing-ephemeraleventrecorder

)

There are a TON of projects over on OSHpark / shared:  https://oshpark.com/shared_projects. since you're filling out a panel I'm guessing you're not using Oshpark - No problem - every project can be downloaded as ready to go gerbers. (pretty damn sweet!)

This way: #Breakout board set