The chess engine environment is rich and evolving. The engines are obviously stronger than ever, and are still improving, both on the software and hardware fronts. Much of the current debate, however, is less about strength and more about what's legitimate and what's not. On the commercial front (read "for sale"), the leaders are Rybka (4), Fritiz (12), Shredder (12), and Hiarcs (13), with the Wikipedia list of such engines including:
Chess Genius, by Richard Lang of Mephisto fame
Fritz, Deep Fritz
The King - the engine of the commercial Chessmaster program
Loop (also the engine for Wii Chess)
Naum versions 2.1 and later
Rebel - (see also ProDeo)
The controversy is not so much with these engines, but rather with the "free," "open source" engines that are cropping up. There are many of these as well, led by what's known as the IPPOLIT family, including RobboLito, Igorrit, IvanHoe, FireBird and Fire. Some have claimed that the IPPOLIT engines are nothing more than decompiled versions of Rybka that have been tweaked (for better or worse) and tossed onto the market. Last I checked, the IPPOLIT authors were an anonymous group calling themselves the "Decembrists." One could also add Strelka to this list and the name Yuri Osipov (a pseudonym?). There's also an open source, free engine known as Stockfish (Tord Romstad (Norway), Marco Costalba (Italy) & Joona Kiiski (Finland)). This last engine has substantial legitimacy in the fact that it's been accepted for rating by the CCRL. The authors may have perfectly good reasons for why they would want to offer this engine at no charge.
I am currently running Rybka 4, Shredder12, Fritz 12, Deep Fritz 12, Firebird 1.2, and Stockfish 1.7.1 JA on my machines. I'm not entirely comfortable with all of these engines, and I do believe that it is in all of our best interests to support only the legitimate (non-prirated) efforts. I do not have the software skills to challenge any of the above programs, and I'll thus be looking to others to offer explanations of legitimacy or otherwise. (Any such claims of illegitimacy have been weak to date, although certainly plausible.) The reason behind the intellectual property protections afforded by patent, trademark, and copyright laws are obvious--to incentivize creativity. Until the answers are clear or more clear, I will continue to purchase the leading commercial programs to support the progress of chess engines, but I will also explore and run my own tests on the engines being called into question.
To the extent that any programmers are taking code from one of the commercial engines and quickly improving it in a pirated release, more issues are raised than just copyright protection. If the commercial programmers are withholding improvements, they may be entitled to the protections of the law, but they aren't necessarily going to get my undying support.