I'm completely out of my element and I'm looking for suggestions. I want to rip all my wife's CD's to her system or to our home server but I'm not really sure which codec/format to convert the files ...

Join them into a single file via a process like this (that link talks about doing it with FLAC files but, IIRC, CueTools will operate on .wavs just as well) Encode to mp3 with generated cuesheet. One ...