If you hop between Calcelmo in Understone Keep (Markarth) and Wylandriah in Mistveil Keep (Riften) they will always have restocked since round-trip is about 54 hours (42 to restock). Wyldanriah is also a short distance from entrance.  

(I should mention Understone<->Mistveil is also very useful when seeking the [Banish enchantment][1] as the blacksmiths are near as well. Oh and remember if you're married these time elapses can be profitable.)

If you're fast on your feet (high stamina, no armor or penalty, Whirlwind Sprint) the jaunt from Mage to General Store in both towns may be worth it.

For my test character (starting stamina, no armor, no shouts) from conversation-tree to conversation-tree:  

Mage->Mage, 1 minute  
Mage->General Store, Riften, 30 seconds  
Mage->General Store, Markarth, 45 seconds (for both running & fast travel to entrance)

I used
`set timescale to 150000` for instant vendor re-stocks, and the mages do carry on average more empty Petty Soul Gems than the general store, just enough that I think my Level 1 is too slow for the complex routes.


  [1]: https://gaming.stackexchange.com/questions/41344