The NY Times had an interesting article about American malt whisky, and how it is expanding the definition of American whisky to include more than just corn and rye, but also barley, the main ingredient in Scotch and many other whiskies. I think it's great that the American craft whisky industry is pushing the envelope and trying new things. Balcone's, a distillery in the article, makes a whisky imparted with Texas scrub oak, the end result tasting like BBQ smoke rather than the sea salt and iodine of Islay malts. Other distilleries are aging in smaller barrels, with wood chips, importing Scottish peated malt, and so on. The article mentions how distillers are distilling beers with strong flavors and hop profile, so that the barley doesn't wither under the American malt requirement of new barrels (it's more delicate than corn). The craft whisky surge is being compared to California wines finally getting their due, and more recently the craft beer explosion. But there are differences.
True, most American whisky is bourbon, and most comes from about a half dozen distillers or so. This is similar to how most American beer comes from BudMillerCoors. The difference is, BudMillerCoors churned out yellow fizzy piss water for decades post Prohibition, due to consolidation, changing tastes, and huge marketing budgets. Blue Moon and other "craft" products from the big three only came out in an effort to strangle the new corner of the market, which is craft beer drinkers. But while Jim Beam's sales are primarily due to their white label--which is on the shelf of almost every bar in the world and could possibly fairly be compared to Budweiser in terms of quality--they have been making their small batch collection, with more intense flavor profiles, for decades. Buffalo Trace's Blanton's was the first single barrel bourbon, introduced in the 80s, and Elijah Craig 12 claims to have been "small batch before the term even existed." In addition to putting out quality products, these major distillers are also innovative. Buffalo Trace has it's experimental collection, which includes made whiskies with rice, wine barrel finished bourbons, etc. They also have one-off entries like the Col. Taylor line (see my review on the Tornado surviving bourbon below), as well as the Single Oak Project and of course, the Van Winkle line.
The biggest difference between craft beer and craft distilling is time and stock. Heaven Hill has acres of rickhouses with more bourbon aging than you can imagine. They can afford to try new techniques and aging practices as long as they keep bottling their standard products. They also have the luxury of waiting for years for products to be perfect, where a startup distiller will use smaller barrels, extra wood contact, and do everything they can to get the product to market to start making profit. A craft brewer can beer made and in bottles in a matter of weeks, but good whisky can take years before it's truly mellow enough for the glass.
All that said, innovation in one corner of the industry is good for the whole industry. Support your local craft distillers. Bluecoat, made in Philly, is my favorite gin. Note that gin, like white whisky, does not need aging time. White whisky's popularity among the cocktail set is another discussion (Whisky Advocate had a good article on the subject, is it a trend or here to stay?). But I caution you, if you are going to buy a craft whisky, do your homework first. Are they buying stock from major producers? Making it themselves? How old is it? What are the reviewers saying? Not all of these questions can be answered by reading the bottle, as image is everything, and brands like to project that 1. they've been around forever and 2. they are handcrafted. Also, none of the answers to these questions determine definitively if the product is good, or more specifically what you think of it. But when you buy craft, you will be laying down a bit more cash on average, and the more educated you are as a consumer, the more likely you will find a winner in your glass at the end of the day.