What format are most people using, and why?

FLAC. Foobar is awesome and I hate Apple products.

I don't understand why you feel 24/96 wave files are the best. Assuming you are ripping CDs, the data must be converted from it's native 16 bit to 24 bit. Wouldn't it be better to save bit perfect 16 bit copies than somehow converting it? If you feel that adding more bits somehow makes things sound better (I don't) then wouldn't it be better to store a perfect copy of the original and up convert on playback? Sooner or later an up-converter you like better will come along and you will be stuck with whatever your old converter produced.

I only use 24/96 when burning my vinyl onto the hard drive. Most of my cd's are burned at 16/44 and I don't like the effects of the up converters I have tried.

That makes good sense. I must have been asleep as I missed the part in your post about analog. What are using to convert your vinyl to digital?

I have a Lynx 2 card in my computer. I also use the Manley Slam (a professional a to d, d to a dac) when I can borrow it. For computer out I go Adobe Audition to the Empirical Off ramp turbo to the Audiomeca Enkianthus X2 ( TRL modified)Dac.