One thing I've done with shoes that aren't quite wide enough in the toe box is to make a cut to allow them to widen a bit.
I'll usually make about a 1-1.5cm longitudinal cut near the base of the tongue of the shoe right where my foot is widest. Many shoes have piece of leather (well, usually imitation leather) running across here. This little cut allows the upper to expand enough that it doesn't bother me anymore.
I've had many shoes go from unwearable to very comfortable with this little alteration. I've also never had any of these cuts run or expand. I have never had problems with that new small opening in the shoe, but if you'd be doing a lot of running in sand or something like that, then maybe you'd want to sew a patch over it, or use duct tape and staples or something.
I've also cut off the tops of heel counters that went up too high and irritated my achilles tendon, and made other small and easy alterations to my running shoes. I've had several people tell me how stupid that is, and that they'd just never buy a shoe that doesn't fit, or that they'd be worried about compromising the integrity of the shoe or whatnot.
My opinion is that if I can make a pair of shoes work better for me, then why the heck not do it eh? No shoe company is producing shoes off a mold of my foot, so why shoes I expect something to fit me perfectly off the shelf.