I have my media files saved in a relative path -a subfolder of my project file (called "audio files", predictably) and all the peak files are stored there with all the wav files.
I like to leave my peak files intact for loading speed reasons (my projects are audio heavy and will take several minutes to regenerate peaks). I don't often have to go digging in the "audio files" folder for wavs (esp since the project bay was introduced) and I just leave the peak files with them, where they are supposed to be.
I have nice clean, organised project folders; the fiddly stuff is tucked out of sight, but intact.
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