To do this you need one of the AGS game released already for linux e.g. The Shivah or Gemini Rue.

1. unpack one of the games to an empty directory
2. remove everything except in the game folder the 2 bin files, the 2 lib directories and its content and the modules.lst
3. install the blackwell games of your choice with wine or unpack them with innoextract
4. copy the Episode* directories to the place where you unpacked the game in step 1
5. create a soft link to the .exe files in the Episode directories named agsgame.dat or rename them to this

if you have done everything right it should look like this:

$ ls -lnR

total 5456
-rw-r--r-- 1 1000 100 141 8. Dez 20:21 agsgame.log
-rwxr-xr-x 1 1000 100 2457884 22. Jul 20:42 Blackwell.bin.x86
-rwxr-xr-x 1 1000 100 2556824 22. Jul 20:42 Blackwell.bin.x86_64
-rwxr-xr-x 1 1000 100 62 5. Dez 22:58 Episode1
-rw-r--r-- 1 1000 100 98865 6. Dez 10:52 Episode1.png
drwxr-xr-x 2 1000 100 4096 6. Dez 10:58 Episode 1 - The Blackwell Legacy
-rwxr-xr-x 1 1000 100 58 5. Dez 22:57 Episode2
drwxr-xr-x 2 1000 100 4096 6. Dez 10:59 Episode 2 - Blackwell Unbound
-rw-r--r-- 1 1000 100 110468 6. Dez 10:53 Episode2.png
-rwxr-xr-x 1 1000 100 62 5. Dez 22:57 Episode3
drwxr-xr-x 2 1000 100 4096 6. Dez 10:55 Episode 3 - Blackwell Convergence
-rw-r--r-- 1 1000 100 94892 6. Dez 10:55 Episode3.png
-rwxr-xr-x 1 1000 100 60 5. Dez 22:56 Episode4
drwxr-xr-x 2 1000 100 4096 6. Dez 10:56 Episode 4 - Blackwell Deception
-rw-r--r-- 1 1000 100 93370 6. Dez 10:56 Episode4.png
-rwxr-xr-x 1 1000 100 75 6. Dez 00:32 Episode5
drwxr-xr-x 2 1000 100 4096 7. Dez 21:45 Episode 5 - Blackwell Epiphany
-rw-r--r-- 1 1000 100 100740 6. Dez 10:58 Episode5.png
drwxr-xr-x 2 1000 100 4096 22. Jul 20:42 lib
drwxr-xr-x 2 1000 100 4096 22. Jul 20:42 lib64
-rw-r--r-- 1 1000 100 192 22. Jul 18:46 modules.lst

./Episode 1 - The Blackwell Legacy:
total 260664
-rw-r--r-- 1 1000 100 319 12. Jan 2012 acsetup.cfg
lrwxrwxrwx 1 1000 100 14 6. Dez 11:04 agsgame.dat -> blackwell1.exe
-rw-r--r-- 1 1000 100 41666393 12. Jan 2012 audio.vox
-rw-r--r-- 1 1000 100 42074966 12. Jan 2012 blackwell1.001
-rw-r--r-- 1 1000 100 5118357 12. Jan 2012 blackwell1.002
-rw-r--r-- 1 1000 100 18822697 12. Jan 2012 blackwell1.exe
-rw-r--r-- 1 1000 100 8 6. Dez 10:58 prog.bwl
-rw-r--r-- 1 1000 100 159196017 12. Jan 2012 speech.vox

./Episode 2 - Blackwell Unbound:
total 212056
-rw-r--r-- 1 1000 100 314 12. Jan 2012 acsetup.cfg
lrwxrwxrwx 1 1000 100 11 6. Dez 11:04 agsgame.dat -> Unbound.exe
-rw-r--r-- 1 1000 100 36257084 12. Jan 2012 audio.vox
-rw-r--r-- 1 1000 100 10 6. Dez 10:59 prog.bwu
-rw-r--r-- 1 1000 100 121376054 12. Jan 2012 speech.vox
-rw-r--r-- 1 1000 100 41571278 12. Jan 2012 Unbound.001
-rw-r--r-- 1 1000 100 3417728 12. Jan 2012 Unbound.002
-rw-r--r-- 1 1000 100 14493753 12. Jan 2012 Unbound.exe

./Episode 3 - Blackwell Convergence:
total 322816
-rw-r--r-- 1 1000 100 319 12. Jan 2012 acsetup.cfg
-rw-r--r-- 1 1000 100 172575801 12. Jan 2012 agsgame.dat
-rw-r--r-- 1 1000 100 27098029 12. Jan 2012 audio.vox
-rw-r--r-- 1 1000 100 12 5. Jan 2012 prog.bwc
-rw-r--r-- 1 1000 100 130863611 12. Jan 2012 speech.vox

./Episode 4 - Blackwell Deception:
total 599272
-rw-r--r-- 1 1000 100 314 30. Okt 2013 acsetup.cfg
-rw-r--r-- 1 1000 100 304040703 30. Okt 2013 agsgame.dat
-rw-r--r-- 1 1000 100 56547139 12. Jan 2012 audio.vox
-rw-r--r-- 1 1000 100 18 5. Jan 2012 prog.bwd
-rw-r--r-- 1 1000 100 253040953 30. Okt 2013 speech.vox

./Episode 5 - Blackwell Epiphany:
total 829784
-rw-r--r-- 1 1000 100 311 5. Dez 22:33 acsetup.cfg
-rw-r--r-- 1 1000 100 281849897 29. Aug 11:23 agsgame.dat
-rw-r--r-- 1 1000 100 14483 8. Dez 21:25 agsgame.log
-rw-r--r-- 1 1000 100 112131703 29. Aug 11:23 audio.vox
-rw-r--r-- 1 1000 100 455678218 29. Aug 11:23 speech.vox

./lib:
total 1232
-rwxr-xr-x 1 1000 100 18532 22. Jul 20:42 libogg.so.0
-rwxr-xr-x 1 1000 100 947460 22. Jul 20:42 libSDL2-2.0.so.0
-rwxr-xr-x 1 1000 100 97232 22. Jul 20:42 libtheoradec.so.1
-rwxr-xr-x 1 1000 100 29172 22. Jul 20:42 libvorbisfile.so.3
-rwxr-xr-x 1 1000 100 159020 22. Jul 20:42 libvorbis.so.0

./lib64:
total 1368
-rwxr-xr-x 1 1000 100 23240 22. Jul 20:42 libogg.so.0
-rwxr-xr-x 1 1000 100 1034008 22. Jul 20:42 libSDL2-2.0.so.0
-rwxr-xr-x 1 1000 100 112088 22. Jul 20:42 libtheoradec.so.1
-rwxr-xr-x 1 1000 100 32416 22. Jul 20:42 libvorbisfile.so.3
-rwxr-xr-x 1 1000 100 192232 22. Jul 20:42 libvorbis.so.0

Btw: I have renamed the .bin files to Blackwell.bin, it looks nicer that way.

To play use the following commands:

$ cat Episode1
./Blackwell.bin.x86_64 Episode\ 1\ -\ The\ Blackwell\ Legacy/
$ cat Episode2
./Blackwell.bin.x86_64 Episode\ 2\ -\ Blackwell\ Unbound/
$ cat Episode3
./Blackwell.bin.x86_64 Episode\ 3\ -\ Blackwell\ Convergence/
$ cat Episode4
./Blackwell.bin.x86_64 Episode\ 4\ -\ Blackwell\ Deception/
$ cat Episode5
./Blackwell.bin.x86_64 Episode\ 5\ -\ Blackwell\ Epiphany/ -gfxfilter Hq2x

The bin file accepts the following arguments:
-windowed Set display mode to windowed
-fullscreen Set display mode to fullscreen
-hicolor Enable 16bit colors
-letterbox Enable letterbox mode
-gfxfilter <filter> Enable graphics filter, where <filter> can be
StdScale2, StdScale3, StdScale4, Hq2x or Hq3x

Have fun playing the Blackwell series natively.

I'm still holding out for a native package build from GOG, but good info otherwise.

Thank you. Great information.

I went a slightly different route.

For that I went to get the AGS runtime and set it up on my machine. Basically what I did was follow the instructions here:
https://github.com/adventuregamestudio/ags/blob/master/debian/README.md

After installing AGS runtime on my system I unpacked every one of the Blackwell games to a separate folder by use of innoextract. After that I created startup scripts for each game, which look like this:

-------------------------------------------------------------
#!/bin/sh
export LD_LIBRARY_PATH=.:$LD_LIBRARY_PATH
exec ags ./epiphany.exe
-------------------------------------------------------------

By the way: That's the extent of a Linux port. If we ever see native packages for Linux their contents will not look vastly different. It will just be less of a hassle to get it running.

I know this is an old thread, but I think it is pretty interesting. Thank you for the info.

I tried to apply those methods to another AGS-based game, "The Cat Lady". However, after extracting the content of the game, I failed to find any .exe in it. What could I have missed?