I will need to update my Free Chess Programs article soon, as the chess engines section is constantly changing all the time.
As far as I know, the best CEGT-rated chess engine at the moment is Stockfish 1.6.3. On a 32-bit operating system and with 2 CPUs, the latest version of Stockfish is rated 3043, a whole 82 points above the free version of Rybka (version 2.2n2) on the same hardware.
The IppoLit family of free chess engines is still not rated by the CEGT Computer Rating List, but word around is that they are even stronger than Deep Rybka 3 (which is stronger than Stockfish). RobboLito, mentioned in my Free Chess Programs article, has now been superceded. RobboLito was surpassed by IvanHoe, which has now been superceded by the even stronger FireBird.
The creators of FireBird state that their goal was to "combine all the best ideas, features, and strengths from the IppoLit family of releases... IppoLit, RobboLito, Igorrit, and IvanHoe". Note that, unlike RobboLito, FireBird is now fully usable in an UCI interface such as Fritz and it now supports multiple processors.
FireBird has an estimated Elo rating of 3400, and even though computer testers haven't tested this engine yet, it is unofficially the strongest free chess engine available.
Nevertheless, I still recommend analysing with Rybka 2.2n2. Even though it has a miniscule rating of 2961, I believe it creates the most accurate assessments of positions. Rybka is known for its modest assessments of positions, making it very handy to use in analysis.
Whilst FireBird and Stockfish may play stronger moves purely on a numeric basis, they do not necessarily evaluate the position correctly. For example, they may assess a position as winning for White when in fact the correct assessment is a slight advantage for White. For this reason, they are less useful for human-assisted analysis.
However, the best way forward, if you have super-powerful hardware, is to run Rybka as the main engine and have FireBird kibitzing in the background.
Note that for people with a single processor and 32-bit operating system, there is a very obscure way to obtain a Rybka 2.3.2a (which is a tiny bit stronger than 2.2n2), detailed in my Rybka article.