Ok I got the ATMEGA16 setup for arduino
I think there are still some issues with it and I'm going to be testing each pin as much as I can tonight to make sure they do what they are supposed to do.
In the end I based it of the Sanguino core and modified that to match the ATMEGA16 and then compiled and tested it. Unfortunately I don't have the code on me now to post - And I'm not sure where to upload it in any case
Bohne thanks for the tip regarding preprocessors I thought that was the case and you just confirmed it for me
And yes I now have a led blinking at me.
I am going to test each of the pins and then I'm going to try and get the STK200 4 Bit LCD going. There is some code around for that so I'm going to try what I can to get it going.