Audiochecker is a tiny and portable tool which analyzes the source of WAV, LPAC, SHN, APE and FLAC audio formats, in order to verify if the encoding is lossless. If not, it means that the files in question are converted from other formats with lower quality, such as MP3.
The project is no longer developed. Last version, 2.0 Build 457 Beta, released in June 2006, can be still downloaded from Softpedia.com
Audiochecker vs Lossless Audio Checker opinions
auCDtect Task Manager is a free GUI tool that lets you check if your lossless audio files were upconverted from a "lossy" file format.Discontinued
Official Website is down and there have been no releases since 2016.
Tau Analyzer is a free program, which can help you to distinguish with reasonable accuracy the original studio-based CDs from poor quality fakes, that have been "reconstructed" using a lossy audio source, such as MP3.
Spectro is a freeware audio file analyzer for windows. Currently capable of reading FLAC, APE, MP3 and WAV files. Spectro lets you view vital data about compressed audio files and creates a spectrogram of the wave data.