I ripped my CDs with dbpoweramp. This is flexible and accurate, it uses a communal database to ensure that your rip is exact. It also automatically gets you cover-art, track names, composers etc. It's free, but buying it gets you better performance on some PCs with more than one processor.
I encoded the files with FLAC, this is an open standard for lossless audio compression that everything should be able to play, even a Mac.
I have about 750 CDs ripped. Using FLAC these occupy 253,879,841,792 bytes, which is I think about 350 Megabytes per CD, which is about half the 'raw' size.
Each 'artist' has a directory, including 'various', then each disc gets a directory and each track is a file. This structure is only really for human use. The player uses the metadata or 'tag's attached to each file which identify all sorts of useful information.
The process is mostly automatic, you put the CD in a PC, let dbpoweramp find the art, tracknames, composers etc then press rip. The directory is created and the job done in a few minutes.