If I was to create an inventory for a magic shop I would think from the perspective of the owner of the shop. (I am going to try to keep this as system nonspecific as possible)
1. Who is he and where is he getting his items?
If he is a Wizard, where would he get healing potions? Does he have a deal with a church or a method of making them?
2. The purpose of the shop is to make a profit, so how does he do that?
a. items accessible to commoners, not necessarily adventurers but might be useful to adventurers e.g. charms to bring good luck, aphrodisiacs, balms, etc
b. adventurer items - oils to improve weapons, buff potions, healing potions (might be marked up if they are coming from a church), etc
c. speciality items - things like this might be hand crafted items designed specifically to be enchanted - wands, amulets, etc. There also might be things like enchanted and protected blank spellbooks, enchanted thieves tools, other enchanted tools
d. practical adventuring items - a cluster of entry level magical weapons and armor, a cluster of entry level wondrous items.
e. a few moderate level items, think 1 or 2 per character class. A higher level weapon or armor, a higher level wand, staff, etc. Not neccessarily everything for every class at this level.
f. 1 awesome item the shops has had on hand.
3. Flavor you can add on top of this is naming the items based on the personality of the owner vs. what they are in the book, including crap. non magical items, or minor the shopkeeper talks up as super powerful, having the shopkeeper knowingly or unknowingly selling cursed items, and/or having exactly what the party wants in the shop window but it is marked sold so they have to somehow talk/force/steal the shopkeeper into selling it to them.
There are a ton of ways you can go with this. I highly suggest you have fun with it and use it as a tool to drive your adventurers.