If you are not registered, do so now, or these will not work.
These are pretty easy. After you've downloaded and (most likely) unzipped one, take the entire folder, not just it's contents, and dump it into the Data folder in your Uplink folder. Start up Uplink, and click the Options button on the main screen. There will be a button called "Edit THEME Options", which you should also click. There should be the list of themes you have in your Data folder. Click the one you want and press the button "Apply". You should see what the theme looks like on your screen. Get back to the main screen, and enter the game. Enjoy!
These are more tricky. The first thing you'll need to make sure you have is a folder inside of the Data folder named "data" and another one named "graphics" (if the new gateway includes custom graphics). These folders are not included with the original installation of Uplink, so you'll probably have to make them yourself. Inside of "data" you'll need another folder named "gateways". Inside of "graphics" you'll need "gateway". Most gateways I've downloaded already have their files in this sort of hierarchy. If so, just make sure the files they have go in the equivalent places. Start up Uplink. Head on over to Uplink Internal Services and you should be able to buy the new gateway. Enjoy!
These work similarly to gateways, but you cannot use an existing save file with them. Uplink creates data on what exists in the world at the start of an account, so you must start a new account every time you install a new LAN. You have been warned. Any existing save files you use will become corrupted and will not work. Anyway, what you'll need is a folder named "lans" inside of the folder "data" inside of "Data" inside of your Uplink folder. Got all that? Basically this is the same as the "gateways" folder you have to have for gateways, except it's called "lans" for LANs. Now, when you create a new account with Uplink Corp, you'll be able to hack the new LAN. There is usually information on how to find it from a read-me file included with whatever else you downloaded. Enjoy!
This is similar to how you you install gateways with custom graphics. You need a folder named "graphics" inside of your "Data" folder, which is inside of your Uplink folder. Just stick in the files and you should be all set. Enjoy!
For Anything Else:
There are other types of mods out there, and they do many different things. It is hard to say what you may need to do, or even if they work. However, just use the same mac hierarchy as the gateways/LANs/graphics use, and it should work. If not, you may have to try several other things, or come here and there may be some people that have the experience to help you out. Enjoy!