Which merchant has the largest amount of gold either in the vanilla game or one added by a mod? The only one I've found so far is the kind of independent merchant that's in an inn in the market district at the IC.

I don't know about merchants added via unofficial mods but http://www.uesp.net/wiki/Oblivion:Merchants link has all of the merchants in the vanilla game as well as the official mods. Some of the merchants via the official mods have a starting gold of 2000 (they go up to 3000 when you reach Master Mercantile and have invested in their stores) otherwise 1200 (2200 at Master Mercantile) is the max unless you want to use Fathis Ules (but he has a few bugs associated with him and he's also a Master at Mercantile which means you'll get terrible deals from him.

Fathis has the most gold at 1500 to start (Although you do have to go through most of the thieves guild)
The Khajitt in the Dark Brotherhood has 400 gold but has a really low mercantile skill so you can easily sell 80% or more of the items worth to him (Useful when selling Welkynd Stones)
Cutter in the Shivering Isles has 1200 gold and has a low mercantile skill (Not as low the Khajitt)
Early on Jensine is a good merchant with 600 gold and she can buy virtually anything execpt for alchemy equipment.