Personally, I don't feel that there is really any company doing a whole lot of "innovating" in the firearms industry. For the most part, everyone is just trying to produce a good product that the market will be interested in. Innovation is really just a buzzword describing evolution. Any real innovation is centered on the military gun space, and even then, they are just re-hashing older design concepts.
In terms of producing fresh concepts and interesting designs, I would agree that Taurus is doing the most in that space. In terms of helping with the evolution of design, S&W is a great model. While gun buyer's are always longing for something new, the fact of the matter is, most are reluctant to actually embrace anything new. Sometimes even properly established and tested items are not accepted by the seasoned gun owner...look at the above comment on the .40 caliber for example. If gun owners are so reluctant to embrace substantive change, then being on top of evolving current technology isn't a bad place to be. You reduce risk while marketing to an audience more interested in reliability than bleeding edge design. S&W is a great example.
The M&P series really stands out as a great evolution of current gun designs. The M&P handguns aren't as "innovative" as Glock was when they were released, but Glock was more than happy resting on it's laurels until the M&P & XD came along. The M&P took a poly design and made it ergonomic with backstraps designed to help fit individual users. The serrations and attention to details on the M&P made it what the Glock should have become, but Glock couldn't bother with. Not "innovative", but certainly a beautiful evolution.
The M&P revolver series is another great example of evolution. In this case, using lighter materials with better tensile strength. In this segment, S&W really owned the market to begin with, essentially competing with itself. If you are already the segment leader, evolution not revolution actually makes the most sense. The revolvers aren't standing still like Glock did with its semi-auto's because they already lead the segment. Reducing weight, adding night sights, and packing more power (.357) in the same size packages may not be flashy, but it certainly is solid. Just ask anyone who pocket carries a J-Frame how much nicer it is to carry an M&P 340 over a 642.
In AR's, well, there's only so much you can do, but S&W offers tremendous value in this area. They offer tactical railed models from the factory along with several other nicely configured setups. Additionally, they are all over the piston market with a very solid and nicely machined piece.
Those are just the M&P series, but S&W is always doing similar things across their product lines. New barrel lengths, custom shop, porting, and a variety of other design tweaks and refinements. Evolution.