Alas, there is no magic answer. You can try some or all of the following:
1) Use an effects loop where possible (my guess is that this is why people use them).
2) Keep the input signal level as high as possible – then you can turn down the gain, reducing the noise by the same amount.
3) Maybe use a noise gate (or a pedal with one) just before the amp if you can find one that is not too noticeable.
