First some general notes. The PKZIP authenticity verification was a feature available to registered PKZIP users. This, presumably, makes it rather rare among electronic distributions of games. Nevertheless it was widely used by Apogee. For whatever reason, FreeCommander makes it very easy to spot archives w/ authenticity verification (more info on that here).
Appending or removing ZIP archive comments does not affect authenticity verification in any way. This means that an archive can cleaned from third-party comments without compromising its authenticity. However, any attempt to add, remove or alter the files inside the archive will result in a warning shown to the user when the files are unpacked (here's an example of a tampered archive). This is why most tampered archives are simply repacks of the original contents.
The latest shareware versions of Apogee/3DR games at the official FTP have authenticity verification. This, however, does not hold true for freeware releases. One notable exception that I have spotted so far is the shareware version of Halloween Harry v1.2. With earlier versions, the situation gets a bit more complicated. Also note that many of the latest shareware versions have earlier distributions with different installers (made by Sub-Zero Software, as mentioned here).
Now, onto the files themselves. Generally, the mirrors of "SimTel, the Coast to Coast Software Repository " (like this) are good source of clean distributions of shareware Apogee and 3D Realms games with early installers. However, not every version is available. ftp.funet.fi is also a good source, but some files lack authenticity verification. Some stuff is also found here.
NOTE: The lists below are incomplete.
3D Realms - shareware releases
These generally seem to have been unaffected by the repackaging tendency (probably due to their size), keeping authenticity verification intact.
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3D Realms - patches
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Apogee Software - shareware releases
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Apogee Software - patches
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Apogee Software - non-interactive previews
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