Obviously the executable and the included service DLL would be different but I am curious as to how the patches compare overall.

I did a bit of a summary on GOG about the patches delivered on the main branch so far and would be interested in how they compare (especially with anyone who has older builds and the .pak files) to the Steam version.

Just some quick notes on differences I do know/remember between GoG Galaxy client version and the Steam version.
v1.04 and 1.05 had fixes on Steam for AMD Phenom that did not arrive till v1.06 on GoG.
v1.09 on Steam had the new threading code mentioned in the release notes but was missing from GoG till v1.09.1.

As far as the easily visible functionality is concerned there have not been noted differences between the descriptions and imagery seen for 1.09.1 Steam versus 1.09.1 GoG.

Here are MD5s for each version released so far to main branch GoG Galaxy Client:

2.0.0.2 - 1.03 - PC Release Version.md5 -- http://pastebin.com/9M8LfbNB
2.1.0.3 - 1.04 - 1284085.md5 -- http://pastebin.com/3cTTBBZG
2.2.0.4 - 1.05 - 1287169.md5 -- http://pastebin.com/Y8xa1uVh
2.3.0.5 - 1.06 - 1289496.md5 -- http://pastebin.com/N2EgE00E
2.4.0.6 - 1.07 - 1314359.md5 -- http://pastebin.com/naqf0NR7
2.5.0.7 - 1.09 - 1337927.md5 -- http://pastebin.com/asrJNig6
2.6.0.8 - 1.09.1 - 1389976.md5 -- http://pastebin.com/3hhYvHfV

NOTE: Game files only I did not include the GOG Galaxy file list, hashdb, etc, nor the MXML or ShaderCache files that get recreated/updated when the game is run.

Here is a list of files changed between versions for the GoG Galaxy Client version:

v1.03 Release <=-=> v1.04 1284085:
Binaries\NMS.exe
GAMEDATA\PCBANKS\NMSARC.25E773B8.pak
GAMEDATA\PCBANKS\NMSARC.2BB4E68C.pak
GAMEDATA\PCBANKS\NMSARC.553AF401.pak
GAMEDATA\PCBANKS\NMSARC.B9700502.pak

v1.04 1284085 <=-=> v1.05 1287169:
Binaries\NMS.exe
GAMEDATA\PCBANKS\NMSARC.25E773B8.pak
GAMEDATA\PCBANKS\NMSARC.4F9B8F8E.pak
GAMEDATA\PCBANKS\NMSARC.553AF401.pak
GAMEDATA\PCBANKS\NMSARC.715AAAD6.pak
GAMEDATA\PCBANKS\NMSARC.7196415F.pak
GAMEDATA\PCBANKS\NMSARC.973CACEA.pak
GAMEDATA\PCBANKS\NMSARC.A11D7F99.pak
GAMEDATA\PCBANKS\NMSARC.AE23BCEA.pak
GAMEDATA\PCBANKS\NMSARC.B9700502.pak
GAMEDATA\PCBANKS\NMSARC.CA1BC01E.pak
GAMEDATA\PCBANKS\NMSARC.CE8DDE7C.pak
GAMEDATA\PCBANKS\NMSARC.DEEEE8A1.pak

v1.05 1287169 <=-=> v1.06 1289496:
Binaries\NMS.exe
GAMEDATA\PCBANKS\NMSARC.25E773B8.pak
GAMEDATA\PCBANKS\NMSARC.CE8DDE7C.pak

v1.06 1289496 <=-=> v1.07 1314359:
Binaries\NMS.exe
GAMEDATA\PCBANKS\NMSARC.25E773B8.pak
GAMEDATA\PCBANKS\NMSARC.2BB4E68C.pak
GAMEDATA\PCBANKS\NMSARC.4F9B8F8E.pak
GAMEDATA\PCBANKS\NMSARC.553AF401.pak
GAMEDATA\PCBANKS\NMSARC.7196415F.pak
GAMEDATA\PCBANKS\NMSARC.973CACEA.pak
GAMEDATA\PCBANKS\NMSARC.AE23BCEA.pak
GAMEDATA\PCBANKS\NMSARC.B9700502.pak
GAMEDATA\PCBANKS\NMSARC.CE8DDE7C.pak
GAMEDATA\PCBANKS\NMSARC.DEEEE8A1.pak
GAMEDATA\PCBANKS\NMSARC.EEAC04FA.pak

v1.07 1314359 <=-=> v1.09 1337927:
GAMEDATA\PCBANKS\NMSARC.25E773B8.pak
GAMEDATA\PCBANKS\NMSARC.2BB4E68C.pak
GAMEDATA\PCBANKS\NMSARC.553AF401.pak
GAMEDATA\PCBANKS\NMSARC.7196415F.pak
GAMEDATA\PCBANKS\NMSARC.973CACEA.pak
GAMEDATA\PCBANKS\NMSARC.A11D7F99.pak
GAMEDATA\PCBANKS\NMSARC.AE23BCEA.pak
GAMEDATA\PCBANKS\NMSARC.B9700502.pak
GAMEDATA\PCBANKS\NMSARC.CA1BC01E.pak
GAMEDATA\PCBANKS\NMSARC.CE8DDE7C.pak
GAMEDATA\PCBANKS\NMSARC.DEEEE8A1.pak
GAMEDATA\PCBANKS\NMSARC.EEAC04FA.pak

v1.09 1337927 <=-=> v1.09.1 1389976:
Binaries\NMS.exe

This info you are taking time to put out here is really handy, so just wanted to say that. Thanks for your effort. :)