I'm more lazy, but do more work.
My media is organized into different directories on different external drives. For movies, if the files are over 4GB, they go into the movies directory on drive 1. If over, then movies in drive 2. One drive is formatted into FAT32 from when I did use the PS3 to playback movies. TV shows go onto drive 1, which TV show directory with subdirectories for each show, and then each season.
I use Plex, and just tell it where where all the movies and tv shows are, and just let it scrape.
I have some directories on my PC, but they're for when I rip and encode. One directory is for output with MakeMKV. I have it linked to Plex to it's own libray. It's to make sure the movie plays. I have another directory for output using Handbrake, which I use to transcode the MakeMKV, so they're smaller mkv files. That directory is also linked to Plex in it's own directory to for testing. I have another Plex library linked to my Media Center DVR recordings.
For metatags, I just manually do them, what I can't set in the ripping or I've downloaded. I find Plex's scraper with IMDB and TVRage to be sufficient for my needs. I just name the file enough--movie title (year) or tv show name - seasonepisode - episode title.
For bonus features, I create a separate directory for them. There is a another Plex Library for them too. I find using the movie setting works best. If it can't find metadata for it, it'll still list the file. I'm too lazy to create my own metadata file. I've been considering deleting this since I almost never rewatch them.