Unless you are transcoding DVDs or pirating videos from the internet, h.264 / MP4 is more or less the current standard for internet videos. If you are ripping DVD / Blu-Rays, unless you are planning on watching them very soon, you're going to need to transcode them anyway if only to bring them down to a manageable size (besides, Handbrake uses h.264)
Started out doing what you do, and moved away once the library grew and became frustrating to reincode, upate the type, fix the metadata (name, series, episode, etc). On a flip side, look at Meta-X to help with the metadata for your MP4's.
What the hell are you doing? Once the video is ripped, it's done. Copy it to an external drive or burn it to a DVD. Just give it a name like "001 - Episode Name" and be done with it. Most media players will read the filename as the video name. No fucking around with metadata required. If you really need to get specific try naming it like "Show Name 001 - Episode Name"