In working on a way to organize the displays at a wine shop it seems that most shops adopt a combination of varietal and regional organization. So, they'll have sections for Chardonnay, Cabernet, Pinot Noir etc. as well as sections for France, Italy, Spain, Germany and so-on.
The goal of every retail set-up is to promote and sell across the entire range of products selected. In the typical set-up, if a customer is looking for Pinot Noir it's very difficult to lead them over to the part of the French section that has the red Burgundy (Pinot Noir) displayed. If someone asks about Malbec, it's tough to lead them to a related wine like Cabernet or Cabernet Franc. I hear from my retail customers all the time, "My South African wines don't sell at all," or "I can't sell French wine to save my life." Part of this is certainly that the customer service staff are not clear on the varietal links of familiar grape types and European regions. It is also the result of dividing varietals across sections while maintaining varietal sections that look complete to the average customer. They're not seeing the full selection but they think they are.
So I advocate a scheme of organization that riffs off wine list organization. Use varietal signs to identify where all the wines of a given varietal can be found together. Given that price points will merge and offer choice, it then becomes less of stretch for a customer looking for Pinot Noir to try a red Burgundy, for a customer looking for a German Riesling to try one from Washington state or for a customer asking about a Cote du Rhone to be informed that other Grenache based wines, from other places might offer pleasing alternatives.
This kind of scheme has built in challenges but they are all good for the store's purchasing disciplines, for sales, for staff involvement and for customer satisfaction. It's still necessary to find strategic spots to keep most of a region's wines shelved together; so, the Italian whites could be shelved alongside the "Pinot Grigio" section, the Spanish reds could be next to the "Tempranillo/Garnacha" section and so on. The varietal signage can be arranged in such a way as to accommodate the most common blends. Thus Bordeaux wines, Claret and Meritage wines would fall between the "Cabernet" and "Merlot" signs.
The wines of the world are varied and there is literally no system that can make it entirely simple. I know of several retailers and restaurant owners who are so concerned with seeming stuffy or high-minded that they choose to be satisfied with leaving out important categories or allowing them to languish, lost to staff knowledge and customer awareness.
A trend in the next decade is the re-emergence of helpful/knowledgeable retail sales ... and I would add restaurant sales. Consumers realize that ratings and recommendations from national publications are of limited practical use. This opens the door for people with passion to reinvent customer service and set up an organizational plan that will gently encourage exploration and product movement. Consumers still want and need guidance but they are finding it more in friendly face-to-face interaction. Price sensitivity occupies center stage with the consumer but there is a large segment, larger among consumers under 35, that wants to find the new and the different. I believe a scheme that integrates varietal and regional organization is the way of the future.