I was the author of the flac plugins before JRiver took them over to include them in the distribution. The last version of flac I used was 1.1.4. The official flac is up to 1.2.1 but the changes are really very minimal and won't affect the losslessness of your files. I'm not 100% sure about the ogg, APE, and MP3 plugins (yes, they use LAME), so I'll leave that to someone else.
The 4k padding block in flac is to reserve space for tags at the beginning of the file, so that you don't have to rewrite the file later. I'd recommend doing it.
Adding more encoders is generally not as simple as dropping in a new dll or exe. MC doesn't just know how to use them. Exceptions: LAME is there in the standard distribution, so you can just copy over it and MC will use it. However, the version being used is the highly recommended one, and it's not recommended to overwrite it. For other encoders, you may be able to use the "external encoder" option, which will look for an external exe file. For best results, however, encoders and decoders need to have specialized plugins written which interface between the encoder and MC. That's what I did for flac before passing the baton. I still have wavpack plugins that are not included with MC on my mcplugins Sourceforge site (as well as older flac plugins).
Am I understanding this correctly ??
What scthom is saying is that LAME is the only encoder that I can replace with a different version if I want to 
The codecs that I use, rather overwhelmingly are Ogg and Flac.
I would like to be able to change the Ogg version as more specialized and sometimes, better sounding Ogg codecs come out on http:/www.rarewares.com from time to time. That is where I usually go to find my audio codecs. For Video, I always use the latest Divx for video.
I use MP3 at times, when when I might be posting some audio on the web, when doing something for someone else as well as use ole MP3 CBR for the audio on all of my Divx videos for compatibility reasons, with stand alone DVD players.
Ogg is my favorite and the Ogg decoder (and Flac decoder), is a native to Cowon (IAudio), portable media players and I am currently using a Cowon D2 as my portable media player, and use it as well to drive video, photos AND music in other devices. Having the power that it has (74w), and a wide ranging equalizer as well as several other options for customizing the output, it sound great when connected to more powerful systems.
On my PC I will tend to play FLAC, because it is on hand as well as the fact that I use it as my "archival" format.
At Rarewares.Org, there are new version coming out that might take advantage of 64 bit processing as well as my AMD dual processor, etc. There are some different versions on the Ogg side that I might like to use inside of Media Player.
Just as a side piece. I just saw a new insane portable media player, the A3, that Cowon has out. All popular open source is native to it, audio and video. It is the first portable player than can record in FLAC !!
All I need is the money for it, but I am very happy currently with the flexibility and great quality of sound (and video), on my Cowon D2.
I tend to like to wait with new software or new hardware to wait until a new version is out, then purchase what was formally the top version, which usually will frop considerably in price and is
field tested. With how easy it is to maintain the TAGS in MC, I like to encode inside of MC. When the tags are coded properly, it makes the organization of files on the Cowon PMPs easier and gives more flexibility. I learned that one the hard way. There are choices to use file names or TAG names.
