Of course, which encoder is "best" is slightly subjective, and certain encoders will work better for different styles of music and at different bitrates. For instance, there's one encoder out there (I can't remember its name) which claims that it's better at high-bitrate encoding (say, 190kbps and above) than the others. It author says that the other encoders are optimized for lower bitrates, and that they don't bother to squeeze out the extra quality that is available at high bitrates. Unfortunately, I don't remember the encoder's name. If anyone remembers it, please post a link in this thread.
About five months ago, I read an article online. It was at a web-zine written for audiophiles. It had the most in-depth comparison of encoder software that I'd ever seen. The author of the article did a very cool double-blind scientific evaluation of all the popular encoders. It involved sending test CDs to a bunch of audiophiles with very good ears. Each CD had three tracks for each test snippet: Original, encoded, and the original again. The listener would then "rate" the last two as compared to the first one. The "double blind" part was that no one knew what order the last two came in until after the experiment was over. Having the original track repeated was the "control".
Unfortunately, I don't remember the name of the webzine that ran the article, so I can't look up the link. Again, if anyone remembers the article, please post a link here.