All GOG games are patched to latests official patch so no need to patch them again. You can't generally even use retail patches with GOG games as they restore any DRM/disk checks retail games had. And I do advice using the unofficial patch as it numerous bugs and improves the AI.

You simply unzip the magic exe and files into the main MOM folder you installed to (the one with a magic.exe in it). Say yes when it asks if you want to replace exisiting files.
Start up the game and you should see the new patch version in the main menu.
It's not perfect, I've encountered some bugs with the G version of the patch (haven't tried the others yet). My issues included
Crash when AI would cast a global spell (I think the spell that allows tech victory)
Also some of the towns in the town list link to other towns. All of this minor of course compared to a better AI.

Dragonsword.com appears to be down, just a day after I found it.

Still down.

You can get the patch from my site. Just go to downloads section. It's in mom folder.

So how well does the new patch play, I haven't got a chance to try it yet.

I used to admin the place without having access to the internal proceedings, that was down to someone else. I have no idea what happened. Hopefully it was not erased for good.
If anyone is looking for the patch, here is a working link:
http://rpgcodex.net/phpBB/viewtopic.php?p=1297140#1297140

Does anyone who managed to get the patch before the site went down have the ability to upload 1.40f? I've been looking to get back into MoM and would really appreciate it if someone still had it.
Nevermind that just found it! Much thanks to Petrell who linked it on his site a few posts back.

Where can I find the g version?

As far as I know 1.40f_fixed is the last version and I believe kyrub announced that he was stopping development. I think there were others who were interested continuing development but with dragonsword.com down there's no way to tell if any of them amounted to anything.

@petrell

Thanks for the clarification.

I am using 1.40f and it makes the game better than "great" now! Funny how you have a game for 10 years and then see modding/unofficial patches for it! :)

Guys, I have some really good news, the problems with AI ships have been finally broken.
It seems AI is now quite competent at hauling stacks on other continents.

It has a downside to it:
I had to increase all transport capacity to max (8 units) and slightly increase the speed of trireme (from 2 to 3) to avoid critical situations. I did increase the Galley speed (from 5 to 8) as well to make it worth. The bugs were numerous and they were really complex issues so I had to take other measures. Hope you don't mind.