Recently I became aware of the PKZIP authenticity verification routine that Apogee built into most of the files it distributed online. Further complicating matters, in quite a few cases the distributions that can be found online (at various FTPs, cd.textfiles.com etc.) are repacks which do not have authenticity verification. It seemed logical to try tracking down as many of the original files as possible.
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 that were found at the 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 (tm)" (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.
Duke Nukem 3D
o v1.0: 3dduke.zip
o v1.1: 3dduke11.zip
o v1.3d: 3dduke13.zip
Shadow Warrior
o v1.0: 3dsw10.zip
o v1.1: 3dsw11.zip
Terminal Velocity
o v1.0: 3dtv.zip (contains SWCBBS comment)
o v1.1: 3dtv11.zip
o v1.2: 3dtv12.zip
3D Realms - patches
Duke Nukem 3D
o v1.0 to v1.1 update: dn3d11pt.zip
o v1.1. to v1.3d update: dnsw13pt.zip
o Plutonium PAK v1.4 to v1.5 update: ppack15.zip
Shadow Warrior
o v1.0 to v1.1 shareware update: sw11swpt.zip
Terminal Velocity
o v1.0 to v1.1. shareware update: tv11spt.zip
o v1.1 to v1.2 shareware update: tv12swpt.zip
Apogee Software - shareware releases
Blake Stone: Aliens of Gold
o v1.0: #1blake.zip (SWCBBS comment)
o v2.0: #1bs20.zip (external comment)
o v2.1: #1bs21.zip
o v3.0: 1bs30.zip
Halloween Harry
o v1.1: #1harry.zip (external comment)
o v1.2: 1hh12.zip (external comment)
Major Stryker
o v1.4: 1majr14.zip
Raptor: Call of the Shadows
o v1.0: #1raptor.zip (external comment)
o v1.1: _1rap11.zip
o v1.2: 1rap12.zip
Rise of the Triad: The HUNT Begins
o v1.0: 1rott.zip (external comment)
o v1.1: found here (SWCBBS comment)
o v1.2: 1rott12.zip
o v1.3: 1rott13.zip
Stargunner
o v1.0: 1star.zip
o v1.1: 1star11.zip
Wacky Wheels
o v1.1: 1wacky.zip
Apogee Software - patches
Death Rally
o v1.0 to v1.1 shareware update: drsw11pt.zip
Raptor: Call of the Shadows
o v1.0 to v1.1 shareware update: rappat_s.zip
o v1.1 to v1.2 shareware update: rpat_12s.zip
Rise of the Triad: The HUNT Begins
o v1.0 to v1.1 shareware update: rot11spt.zip
o v1.1 to v1.2 shareware update: rot12spt.zip
o v1.2 to v1.2a shareware update: rot12asp.zip
o v1.2 to v1.3 shareware update: r13swpt.zip
Stargunner
o v1.0b to v1.1 shareware update: sgsw11pt.zip
XenoPhage: Alien Bloodsport
o v1.0 to v1.1 shareware update: xpsw11pt.zip
Apogee Software - non-interactive previews
o Bio Menace: 1bm-pix.zip
o Blake Stone: Aliens of Gold: 1bspix3.zip
o Boppin': 1boppix.zip
o Hocus Pocus: 1hppix.zip
o Monster Bash: 1mb-pix.zip
o Mystic Towers: 1mtpix.zip
o Raptor: Call of the Shadows: 1rappix.zip
o Rise of the Triad: 1rotpix.zip, 1rotpx2.zip
o Wacky Wheels: 1ww-pix.zip
o XenoPhage: Alien Bloodsport: 1xp-pix.zip