Fundamentally, lower values have higher cutoff's in terms of frequency when in a bypass is used in a signal path as a coupling capacitor. So a 1.0uF cap would allow frequencies lower in value to pass through (better bass) than a .01uF cap. Generall signal path caps are relatively small in size, like 1.0uF or .47uF, so you would need to bypass them with something even smaller, like a .001uF cap. But bypasses affect the high frequencies only in this instance. I have commonly seen people use larger value coupling caps than prescribed for better bass response and then using a bypass for the higher frequencies.
There's also issues of planned low frequency cutoff in phono stages where the size of the cap acts like a wow and flutter filter of sorts.
In a power supply I don't think the value is overly critical, as long as you keep the 1000 to 1 ratio or larger in mind. So bypassing a 100uF cap with a .1uF cap is appropriate, but a .01uF bypass is also OK.
I'm sure the engineers here can give you far more detail than I can. But this is what I've found in practice.
Bob
