I've been using iSub for a very long time and have always been annoyed by sudden volume shifts from track to track. I'm very happy to have found this one step solution. oggenc2.exe can do the entire job. It does not need any other file to work even though the help file suggests you need flac.exe in the path.
"oggenc2 -Q -q 7 --FLAC-scale 1 %s -o -" This utilizes track gain
"oggenc2 -Q -q 7 --FLAC-scale 2 %s -o -" will apply album gain.
There is no way to apply Smart Gain in iSub, so go with your usual listening habits.
There may be some technical reason why this is not a perfect application of replaygain. All I can tell you is that the sudden shifts in volume are gone.
You can find various versions here:
http://www.rarewares.org/index.php
I am using Oggenc2.88 using aoTuVb6.03 (Lancer Builds) for x64 in Subsonic 6.1.5