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GOG sells version 2.1 while the latest is 3.0
Okay, I can confirm this. Just loaded up Aliens of Gold and it says version 2.10R which matches that shown on the Aliens of Gold gamecard page. Looking on the 3D Realms website, though, shows that there is a patch available to update from 2.1 to 3.0. The file can be downloaded here:

http://www.3drealms.com/blake/index.html

It says it is a maintenance release but doesn't say what it fixes.

Anyone got any info on what it does? Anyone installed the patch through DOSBox?

Ultimately, I'm guessing that GOG support will need to be made aware of this (they may even know already).
I've raised a support ticket to GOG support now. :)
Good work soldier :)
According to an earlier thread there is no functional difference between the two versions and the 3.0 version introduces a minor issue with shareware details showing up in the full version. It looks like GOG having the older version may be intentional.
Well in that case...
3dr did answer that the 3.0 patch was to update the "read this" section to show the most recent price list and contact info for resellers. there is an bug on the patch where the registered version uses the shareware menu background that has the price to upgrade to the 6 episode version. to prevent the GOG.com copy from having an old ad on it joe seagler gave gog.com the 2.1R version witch is the last game play patch
Makes sense
3DR basically decided that since both had really out of date catalog info there was no real problem giving out an older version. if they had the code still the art could be updated. like ID does with wolf 3d to remove the apogee logo and replace it with the current publishers logo.
For those who really want the final version, 3.0, there's a tool that can patch it for you.
You can get it here. Also, on the very same page there is a source port for Wolfenstein 3D which is currently the best source port for that game. It will also support Aliens of Gold and Planet Strike in the near future.

http://maniacsvault.net/ecwolf/download.php

DO BE AWARE THAT OLDER SAVES WON'T WORK AT ALL WHEN THE GAME IS PATCHED!
Post edited July 31, 2013 by Ghostbreed