For protoboard, I use tin snips almost exclusively. But this is because the largest protoboards I have are very small. I only ever use protoboard to hold 1 or 2 components. So I take small boards and cut off even smaller pieces. Since this is invariably happening at my bench while I'm making something, I usually just file the edges smooth with a regular steel hand file.
If you create large circuits on protoboard, score and snap works great.
A good way to cut a lot of FR-4 in straight lines is a wet diamond saw (tile cutting saw). But I graduated to using a router table with 45 degree tilt using a carbide end mill. I'm not sure this latter thing exists as a finished commercial product, where the end mill can extend far enough to reach. (If you can buy this lift, it will cost a lot of $$$, not to mention the cost of a table and a router). I have custom made table for small rotary tool, and this is bomb. I am not sure how much FR-4 a carbide end mill can cut like this, but it is a heck of a lot. Been using the same 1/8" endmill for years. A v-cutter bit will wear out in a blink.
For cutting weird shapes, using the side of an endmill is superb. But using the corner of the endmill tilted at 45 degrees is extremely fast and smooth for scoring/cutting square panels, and there's no danger or dust (or water spraying at you) as with a circular carbide or diamond table saw.
For cleaning up straight edge of FR-4, after cutting it at 45 degrees, I use a disc sander. I might finish by just touching one side on the router because it gives automatically perfect parallel edge on the opposite edge, when you use a fence on the reference edge.