How do you incode your digital media?

Looking at my options here. Has anyone experienced any problems with the "lossless" forms of media storage? Any differences in fidelity that only us audiophiles may be bothered by? I am looking to incode everything in Apple Lossless, as it seems to be the most recognized and should integrate with a Squeezebox 3 nicely.

Let me know if you have any thoughts!

Ben