You can use the atempo filter in ffmpeg 1.0 and later:
ffmpeg -i input.wav -f:a atempo=1.25 output.wav
atempo
only accepts values between 0.5 and 2.0, but you can bypass the limitation by chaining multiple filters:
ffmpeg -i input.wav -f:a atempo=2,atempo=1.5 output.wav
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