Getting spare keys working on the MK4 platform can be a bit of a nightmare at first glance so here are a few pointers:
Key overview:
There are four types of key on the MK4 platform all have an immobiliser transponder fitted to facilitate starting the vehicle.
1. Standard non-remote key
2. Emergency key (plastic):
3. Two button remote early type:
4. Two button remote late type:
The two button types can be seperated in two by grasping the key firmly in both hands and pulling the two halves appart, the top half with the buttons contains the remote control for locking and unlocking the car and the bottom half has the key blade and immobiliser chip inside.
Top
Bottom
The immobiliser chip is highlighted in red in the last picture, these are made of glass and are very fragile - they are glued into the original VW keys and are next to impossible to remove without breaking and once cracked they don't work.
Spare Keys \ Remotes
1. Remotes (top half of key)
If you want a new \ replacement remote fob then you need to make sure that the part number and frequency of the remote matches your current key fob. The replacement key fob can be a used item.
To check your current key frequency you need to seperate the key in half then turn the top half over, on the back is the part number and frequency info
There are two frequencies make sure you get the correct one!
2. Keys (bottom half of remote key or standard non-remote type key)
As the key bottom half contains the immobiliser chip there are a few things to look out for when buying a new \ replacement key, as keys that have been coded to an immobiliser 3 vehicle can't be recoded to a new vehicle as the chip is write once.
Ideally buy a completely new key that has not been coded to another car before.
If your car is immo2 based:
You can buy a second hand key but you will need a new key blade to be cut, however the key can't have come from an immo3 vehicle as it can't be recoded
If you car is immo3 based:
The immobiliser can't be second hand (used), you will need a key bottom with a virgin transponder fitted to enable it to be coded to your car. So that means either
- A brand new key bottom half or
- A Second hand one with a new blade and then you will need to get a new transponder sepperately, Hickleys sell the transponder (AKTP2).
Beware on eBay when looking at keys, the add may say new key blade fitted, this however does not mean that the transponder chip is new and uncoded so you might end up with a key that unlocks the car but can't be coded to start it afterwards - If in doubt explicitly ask the seller if the key has been coded to a vehicle or not and does it contain a virgin transponder.
If you need a new key blade for a key there is a seller on Ebay that supplies new blanks cut from a digital photo 
Once you have your new key it will need coding to your car, you will need the SKC (secret key code) to match the immobiliser chip to the car but you don't need the SKC to match the remote part for locking and unlocking the vehicle, some older cars had the SKC provided on the key tags that came with a new car. If yours didn't then it can be retrieved with some third party tools such as Vagtacho.
VCDS (VagCom) can't retrieve the SKC code
Hope that helps
Neil