[Richard Crowley]

"Dave" wrote ...
I have been disappointed with the audio quality of some CDs I have
bought recently.

This has been discussed many times in the recent past.
Note that far and away the prime suspect is hyper-compression
(compression of the audio levels, NOT data compression of the
signal stream.)

Is there a free program I can use to get an accepted
measurement of fidelity? (like a signal to noise ratio)

1) SNR is not "an accepted measurement of fidelity"
2) There is no specific "accepted measurement of fidelity"
"Fidelity" is a combination of many things. Some subjective.
3) It would be difficult-to-impossible to actually meausre SNR
on a commercial CD because of the way they are mastered.
(i.e. there is no "baseline" because it is usually muted)

I have my suspicious that some may have been stored an MP3s and then
"unripped" in the factory. So how can I tell for certain if my CD has
been an MP3, or other lossy format? I'd hope mp3 storage would leave
different markers than the original tape, for example.

Did you buy these CDs from the back of Guido's white van?
Do you know they are legitimate and not pirated copies?
Seems very unlikely that commercial CDs would have ever been
processed through any such gross lossy step as MP3 compression.

To get a good measure I'd expect some Fourier transforms and signal
analysis to be done, so this should be relevant to sci.physics.

It has been discussed here before that there are relatively easy ways
of analyzing audio to detect lossy compression such as MP3. Many
people claim they can hear it easily.