Monkey's Audio in MC is the latest. It was upgraded from 3.97 to 3.99 some months ago. That's easy because there is only one source for it (Matt) and there are also no audio quality differences in lossless.
LAME situation is quite mixed. Biggest version number is not always the best in the terms of audio quality and the situation can change with different music samples. One well-known "authority" here is Hydrogen Audio Forum (
www.hydrogenaudio.org). People there are constantly making ABX listening tests with different versions and compilations and the developers are contributing the forum. Their consensus is that the best audio quality for high bitrates is still in version 3.90.3 (with Dibrom's switches - read about it there) although the latest from 3.91-3.9x series - stable LAME 3.96 is out. 3.97 is still at alpha stage and it is intended only for testing.
MC uses internally 3.93, which is a good choice, but better would be 3.96 because there are many enhancements to speed and quality and no known bugs. Versions 3.94-3.95.1 were not so good.
I suggested here some time ago that JRiver could safely upgrade internal encoder to LAME 3.96. In my opinion they also could default
--preset settings, because those make the best quality encodings and not everybody is aware enough to learn about them by their selves.
I use 3.90.3 as an external encoder for the quality reasons. Sometimes I change to 3.96 because it's almost twice as fast when making VBR encodings.
I have recently interested about Ogg Vorbis too and I have made some testing with oggdropXPdV1.7.11GT3b2 encoder. There are also many different versions and compilations of Ogg Vorbis encoders. Internal Ogg Vorbis encoder in MC is not any of the newest versions.
Musepack (mpc) situation is quite simple. Most enthusiasts are using mppenc v.1.14 beta (it has been out a long time). There is also version 1.15r alpha. MC uses internally version 1.1, which is the latest "non beta", but generally considered old.