As a runner I know this pain too well.
You are probably buying your shoes a bit too short (even if it's the size you used to/have always worn, and/or it seems to fit fine in the shoe store, and/or you have other shoes this size that fit).
Remember with running shoes, sizes are all over the map (they're as bad as dress sizes in that regard), and dress/street shoes are only a little better. I have 7.5 street shoes that fit well, and 8.5 running shoes that give me black toenails (they seemed like a good fit in the store...). I also have street shoes that fit well across that whole size range.
Another thing to keep and eye on -- toebox shape and volume. Some athletic shoes either have a pronounced curve, or are extremely straight, and either of these can cause toe problems (for either the smaller toes in the first case, or the big toes in the second) if the variation from your foot shape is too great. Some shoes -- curved or not -- taper significantly in width from the ball of your foot to the toe, which can lead to toe issues. Some toe boxes taper excessively in height/volume (that is to say, the height at the very end is MUCH smaller than the height over your metatarsal area), and this can be a problem too (usually is for me).
Sometimes a badly placed seam or overlay in otherwise well-fitting shoes can cause tremendous grief as well...
A good rule of thumb for running shoes is that, standing or sitting, you shouldn't feel the edges of the shoes or any overlays on any of your toes, and you should have at least a thumb's width of distance between your longest toe and the end of the shoe (if the toebox is low volume you'll need more than this, and may want more anyway). For girly pointy shoes with heels, well, you just have to decide how much discomfort you're willing to bear (I think it's a hard line to find)...
Good luck!!!
Oh, are your cycling shoes causing discomfort? I wasn't sure from your post, it sounded more like your cycling shoes are just exacerbating pain from other shoes... But that's something to think about too. Even though cycling shoes can be much tighter/shorter than other shoes, toebox volume is still important.



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