Check merchants periodically; depending on the NPC, they restock after 10 or 15 minutes real time.
George at the start of the game can have potion bottles, otherwise check Blake and Tingalf, etc, in Ars Magicana and Corinna, Mpenzak and the doctor / potion seller in Verdistis.
If you quick save before running your mouse over an item/chest/merchant or hitting the alt key, you can identify the item or trade with the merchant, then quick load to get different stats or inventory. This can be done repeatedly to get the best stats or specific bonuses on an item (save after finding good candidates) or looking for specific items (such as spellbooks or charms) from merchants. Unless you really need potions, don't waste too much time with this, though (in general, it really isn't necessary to get the best possible equipment).
Mid to late game you could try Heaven's Gift, if you have the skill points to spare. On level 3 it starts giving normal sized potions, so as long as you have enough mana to get at least one restoration potion (or health + mana with level 1 Alchemy), you can cast it until you run out of mana and refill. By then you may have enough of a stockpile of potions that random loot is good enough for empty potion bottle, or buying the ones that show up at merchants when selling loot, etc.
Alternately, you can cheat.
Once you have 2 potion bottles (or anything else stackable), drag a stack out of (or into) your inventory (or container) and hold down the control key before dropping. This will bring up the split stack pane; type in a negative number and hit enter (the checkmark will be greyed out). This can also be done in the trade window.
