When I first started doing this blog, I selected my snacks mainly from what was in the local markets. It was easiest just to peruse the snack isle and select something while dealing with my usual food shopping. As I continued to write posts and do research, I noticed that a lot of the newly released items that were turning up on manufacturers' web sites weren't making their way onto the shelves in my local markets. In particular, very few of the plethora of new KitKats were on display, but also a lot of "limited edition" specialty items were absent.
The marketing in Japan is fairly specific and all (Tokyo) shops are relatively small. That means that it's difficult to get all of a particular company's product line-up on the shelves at one establishment. Unlike the U.S. where you will see aisles full of every variety of Cheerios ever cooked up by General Mills in one place, you have to find the proper outlet for a particular item in Tokyo. If the market is geared toward older folks, children and housewives, it'll show up in the markets. If it is targeted at young women, business men, or single people, it is most likely to show up in convenience stores.
Most of the novelty flavors of popular brand names are marketed toward the bored people who work in offices and peruse convenience stores at lunch or tea time. Things like Pepsi White are less likely to show up in supermarkets and far more likely to spend their brief time on this earth in the refrigerator cases of 7-11. These flavors cater to boredom and a hunger for novelty rather than a permanent place in the stomachs of consumers. You can take a new find back to the office and share it with coworkers then compare notes on how obnoxious it is.
If you're looking for the new, weird things that are usually covered in the quirky Japan sites and news, the convenience stores, especially places like Family Mart and 7-11 are your best bet. If you're interested in more old-fashioned or daily snacking possibilities, then you're better off hitting the markets.