So, here's what I've discovered with my little foibles with Creatures Docking Station:

Change your shortcuts

* Always run the applications via the engine.exe file. The Docking Station shortcut installed on your desktop will by default try to use InstallBlast.exe, which does not function now that the servers are offline -- it will ask you if you want to download an update. This should throw a red flag for you because the version number it suggests is blank. If you attempt to download the updates, your installation may throw errors on startup!

Resolution, full screen, and bit depth (16-bit colour warning)

* If the applications run in fullscreen mode, your graphics card *should* take over the colour switching for you, so you won't have to reduce your colour quality settings on your system. Look up the user.cfg file in the installation folders and, if you don't see the "FullScreen" line set to 1, change the 0 to 1. This will let you run the game at its old, classic resolution. If you want to run it at a modern resolution (such as glorious 1920x1080p -- yes, it works!), you will have to run it in windowed mode. Unfortunately you will need to reduce your desktop graphics to 16-bit colour to do so. This depends on your video card so unfortunately I can't list every solution here -- on an ATI card running Catalyst 12.4, you can right-click on your Windows desktop to open the Catalyst Control Center and open the Desktop Management->Desktop Properties submenu, where the "Color quality" option will then give you the ability to drop down to 16-bit. Just remember to fix it after you're done!

* If you want to automatically switch to 16-bit colour before running, more advanced users can use one of the 32-bit builds of the qres (QuickRes) utility available in the source code release of qres (http://sourceforge.net/projects/qres/files/qres/QRes%20source%20code%201.0.9.7/). Simply extract all of the files contained in the "\qrescd\sample-cd\qres" folder inside the zip file into your Docking Station and/or Creatures 3 folders, then create a .bat file containing the following:

path_to\qres.exe c=16
engine.exe
::Change 32 on next line to whatever bit depth you normally use (32 for most people these days)
path_to\qres.exe c=32

Then run the .bat file to start Docking Station or Creatures 3 and it will automatically switch your resolution to 16-bit colour while running the game, and then automatically switch it back after you're done! (Note: you may experience a black screen -- don't be alarmed (I know I was!). Either give it a few seconds, or hit Alt+Tab to switch to another window and then hit Alt+Tab again to switch back.) Mad credit to a fellow aptly named TheDoctor on this thread for the tip. Yes, this works for me and is now what I use.

* When windowed at massive resolutions, edge scrolling no longer works. Keep your keyboard handy to use the cursor keys, as that will let you move around, or use the middle mouse button to drag the screen.

Installation folder

* By default Docking Station is installed to "C:\Program Files (x86)\GOG.com\Creatures Exodus\" (on a 64-bit system) or "C:\Program Files\GOG.com\Creatures Exodus\" (on a 32-bit system). In general, DO NOT CHANGE THE INSTALLATION FOLDER or Docking Station may have difficulty detecting the Creatures 3 installation. If you do change the installation folder of Creatures Exodus, look in the folder where Docking Station is installed into and find machine.cfg. Look for these lines:
"Auxiliary 1 Backgrounds Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Backgrounds\\"
"Auxiliary 1 Body Data Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Body Data\\"
"Auxiliary 1 Bootstrap Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Bootstrap\\"
"Auxiliary 1 Catalogue Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Catalogue\\"
"Auxiliary 1 Exported Creatures Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\My Creatures\\"
"Auxiliary 1 Genetics Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Genetics\\"
"Auxiliary 1 Images Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Images\\"
"Auxiliary 1 Overlay Data Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Overlay Data\\"
"Auxiliary 1 Resource Files Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\My Agents\\"
"Auxiliary 1 Sounds Directory" "C:\\Program Files (x86)\\GOG.com\\Creatures Exodus\\Creatures 3\\Sounds\\"
You will have to ensure that all of the folder names match the real folders on your hard drive. If you do not have these lines in your machine.cfg, make sure you add them and set them properly! Be careful with the backslashes -- they must be "escaped" (doubled).

Login disabler (IMPORTANT!)

* As Docking Station servers are no longer online, you will need a login disabler. Open up your Docking Station folder and browse to the "Bootstrap"->"010 Docking Station" subfolders. Find the file "zzz_gamestart_login.cos" and rename it to "zzz_gamestart_login.cos.bak" to save a backup, then install one of the login disablers available.
DS Offline Option: Official from http://www.creaturesdockingstation.com/ (Hotlink)
MNB Login Disabler: Originally from Creatures Mainframe, now down -- mirrored at http://mythwoods.treesprite.com/treesprite.com/mythwoods/viewtopic.php?f=43&t=973
Hands-on/DIY: Do-It-Yourself info is available on the Creatures Wiki

* If you'd like, the free Creatures 1 to DS Patch also provides a login disabler. This isn't recommended for everyone since there are some things it is incompatible with (like the WIP Creatures *2* to DS patch...), but if you're interested, you get (most of) the original Creatures 1 content in the modern Docking Station system -- much less gloomy and almost as pretty! There are some minor bugs and inconsistencies in the content, but that shouldn't hold you back. Also available from the Creatures Wiki.

NEED MOAR STUFF

* A lot of the official GameWare Development tools are still online, but you will have to change the .co.uk in various URLs to be able to download them. Some other files are not available even on the GameWare server, but I was able to get them through everyone's favourite internet resource, the archive.org WayBackMachine.
Browse through http://www.gamewaredevelopment.com/cdn/cdn.php?product=c3ds and any time a link doesn't work, check to see if it changed the domain from ".com" to ".co.uk". If it did, copy and paste the URL into a new window and change it back, and you should get your file!

* You will most likely have to install the Creatures Remastered patch to be able to use the official tools -- otherwise they will report that you do not have the game installed. Get it at AmberCreatures.