As for Phantom Menace, I alternate between the official Video CD release (Sadly I accidently bought the Hong Kong version instead of the Malaysian release, which means I am stuck with hardcoded Chinese subtitles) and the “TB” Digital Broadcast preservation. Video CD is low quality and Pan and Scan, but I appreciate it being an official release. TB is just excellent. It is the real DVD version to me. Pretty much flawless.
I do have that Chzech (?) 35mm print scan, but those are not really my thing. Color correction can always be finnicky, the image might not be completely stable, etc. Many variables where the one scanning it has to make certain choices.
Watching digital versions just gives me peace of mind. Even if the quality is bantha poo, I can rest assured that the bantha poo is not tampered with (In case of the VCD. TB looks really good).
I cannot really speak of Clones and Sith, as the changes are really too small for me to bother with non-DVD versions.