After searching for information on how to change the prices of shops (and finding nothing) I decided to search ff7.exe with a hex editor. Progress has been slow, but I think that I have stumbled across some data for prices in shops. At 0x523B8C in my patched ff7.exe (official patch and chocobo patch) there are some hex bytes with seem to correspond to the prices of Cid's weapons (and the data starting at 0x5219C8 is dialogue from shops - what, I wonder, are the spaced-out bytes from 0x521E18 to 0x52381D?). There are lots of other bytes in that part of the file that look like prices as well. I'll do some more searching tonight; who knows what will be found? Maybe nothing, maybe something; maybe someone else might have something to add...
My apologies if all of this has already been discovered and I am reinventing the wheel.
EDIT: They ARE prices: I changed the prices for potions and Phoenix downs
EDIT2: RESULT! EUREKA!
I was looking for the prices at which master materia could be sold, but couldn't find anything of which I could be sure. Then, an idea came to me: why not mash the numbers on my keyboard like a hyperactive five-year-old and see what happens? I did, and when I loaded the game, the prices for master materia were FUBAR (the R standing for recognition - I made a backup, of course).
It turns out that the prices from master materia are from 0x523E58 to 0x523FC3 - the price is the decimal conversion of the hex bytes x 70, so "All" materia (at 0x523EB4) is 1 400 000/70, or 4E20 (shown as 204E in a hex editor). I changed it to 7D0, and now mastered "All" materia sells for 140 000 gil.
EDIT3:
Those "spaced-out bytes from 0x521E18 to 0x52381D" are, as I should have known, the items and materia that the shops sell, and also determine the text at the top of the screen in some way. By changing 0x521EE0 from 31 to 50 I managed to get the materia seller in the Sector 7 slums to sell "Leviathan" materia instead of "Fire".
I'm waiting nervously for someone to reply "we found this already!"