sox input-file output-file speed 1.001001001001001
where files can be WAV or AIFF. Sox works out internally that the decimal is in fact 1000/999, so the timing adjustment is 100% accurate (and the resampling is high quality). Going the other way is of course
sox input-file output-file speed 0.999
FFmpeg can also do it accurately timewise, but its resampler has had some quality problems. Version 1.1 can use the sox resampler (see here: http://ffmpeg.org/trac/ffmpeg/wiki/FFmpeg%20and%20the%20SoX%20Resampler) but its probably simplest just to use sox.