As far as I can tell, Replaygain is an MPC thing. So how come the FLAC Winamp 2 plug-in has an Replaygain? Hell, I'm not even sure how Replaygain works or does. Search results still left me confused.

There isn't a format I can think of that can't be RG'd (either natively or as a wav before encoding...ie WavGain). Foobar can RG any file it can play AFAIK. I'm not sure if there is a direct FLAC RG'er. Some RG'ers actually alters the data in the file (MP3Gain & WavGain). Others (such as VorbisGain) puts the gain values in the tags and relies on the player to pump up the volume. Newer version of MP3Gain can do either (I've heard).

xen-uno

ReplayGain is an technology of setting volume level between tracks to achieve same perceptible loudness.
It can be applied to any encoding algorithm - look up MP3Gain, WaveGain - not to mention VorbisGain (OGG), ReplayGain for MPC and ReplayGain for FLAC. MP3Gain and WaveGain really change the data in the file
(MP3Gain actions are losslessly reversible - it changes a flag in MP3 headers),
other formats require support in the player, as they store volume levels in tags (nothing changes in the file).
MP3Gain isn't very accurate due to MP3 format constraints (works in 1.5 dB steps).

All ReplayGain tools try to achieve percieved loudness at around -89 dB - this is somewhat quiet,
but allows ~6 dB peaks.

actually flac can encode and track-rg in one step. (in cmd: flac filename.wav --replay-gain)