Einstein did not wear socks, reportedly because he didn't like the way his big toes poked holes in them. I recently scored some brand new New Balance sneakers for half price at my favorite thrift, in my favorite width size (4E) made on the SL-2 last (NB nerds will understand).
My big toes always poke holes in the mesh fabric of my NB sneaks, likely because I rarely wear socks and I like my shoes a bit oversize. So I got some soft, thinnish leather to use as prophylactic patch material and some leather glue, a marking pen, scissors and some plastic bags to use for stuffing.
When I first tried patching my sneaks, I applied the leather to the exterior fabric (d'oh, I'm no Einstein). It sort of worked but was ugly and the edges were exposed to snagging and ungluing. I soon pulled the patches off and reglued them on the inside of the shoe. This had the nice result of repairing the torn fabric so well that you can't tell that there were once holes in the mesh.
Step 1: Cutting the Patch
After gathering your materials, cut a patch sized to match the front of the toe box area, guesstimating where the patch will best fit. I try to aim for the sewn end of the tongue for one edge of the patch and the rubberized toe area at the front of the mesh for the opposite edge. Mark and cut or just eyeball it. Pen marks and uneven cuts won't matter since the patch is inside the shoe.
Flipping the first patch upside down will make a tracing suitable for the opposite shoe. I think - it really doesn't much matter and two identical patches will work fine.
Step 2: Glueing and Inserting the Patch
Do any final trimming as needed and apply your leather glue, paying special attention to the edges. Then move the shoe tongue out of the way (for the easiest access, remove your laces). Grab a gluey patch by the tongue end and slip it into the toe box. You can tell by feel where the patch edges are in relation to the tongue and tip of the shoe, and sometimes you can see some of the glue ease into the mesh. Adjust as necessary. If the patch feels really lumpy somewhere, take it out and trim it some more, or flatten out any wrinkles, freshen the glue and try again.
Now grab something to stuff in the toe box to apply pressure to the patch and to hold the patches in place until the glue dries. Plastic grocery bags are less likely to permanently glue themselves to the patches, but crumpled up paper will work fine. I like to wait a full 24 hours for the patches to dry. My Fiebing leather glue just says to apply pressure until the glue dries.
Step 3: Stuffing the Box and Watching Glue Dry
I don't know how this repair compares to using something like Shoe-Goo. My guess is that a thin patch is smoother. That said, if you wear a snug shoe, you could experience toe rash. And if you're a runner, you'll probably just want to let your shoes wear out and enjoy the extra ventilation your toe holes provide until you replace the shoes.
Sorry, I haven't tried making HydeTheJekyll's cheap boroscope, so there aren't any pics of the patchwork inside the shoes. :-)