Bukkit

As of 1.3 you can have each shop have a unique number of slots for the shop. All you have to do is add this:

Slots: [Number]

Due to the way Minecraft handles interfaces the number of slots must be a multiple of 9. Also note, you don't have to set the number of slots for every shop, if you don't set anything it will default to whatever you have in your config file. So this is how a shop yml would look with 9 slots.

Slots: 9
Slot0:
    ItemID: 43
    ItemAMT: 1
    TokenCost: 1
    GiveItem: true