For taking my DVD episodes to HDD I've been storing each episode as a single VOB file. That way I can retain alternate audio streams as well as subtitles. I use DvdShrink to do this, and just check the option NOT to split at 1gb.
If I need to do HD or want to go Mpeg4 with the recordings I use AutoMKV
http://forum.doom9.org/showthread.php?t=113811 I used to use AutoGK, but I find I get much better results now.
[Edit]
Since I've seen mediaportal touched upon of late, there is a great MyTvSeries plugin that will aggregate all the episodes in a directory and go fetch the individual TV synopsizes along with banner art. When you go to watch them, if you haven't watched the episode before, it will keep the episode info hidden to prevent spoilers, and then open them up next time. It's very slick and I mention it only to express my interest in something like potentially making its way to what I use all the time
Making it easy to catalog all of these shows would be a lifesaver. (Truth be told, I use the plugin to retrieve the data for me, and then copy it into a custom DB over here... shhhhh)