Spectrum!

auCDtect Task Manager is a free GUI tool that lets you check if your lossless audio files were upconverted from a "lossy" file format.

Lossless Audio Checker is a utility to check whether a FLAC or WAVE file is truly lossless or not, by detecting cutoff frequencies. It can show you the full frequency range for each file.

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.

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. Using this program you can check the authenticity of your purchased or borrowed music CDs. Tau Analyzer features an intuitive user interface, allowing users to work directly with audio CDs, and has some additional functions such as a Spectrum and Frequency analyzers, ATIP and ISRC data readers, etc. »

sndpeek is just what it sounds (and looks) like:

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. This allows you to quickly and easily spot quality issues with a file and also look for transcodes.