<p>I'm relatively new to Nant, what i'd like to do is have a task that creates a new Website and AppPool in IIS6</p>

<p>is there a way to do this in Nant?</p>

<p>Essentially the task would need to set all the appropriate properties including the correct version of the .net Framework</p>

<p>Ideally i'd also like to check if the site is already present in IIS.</p>

You can do this from the command line using ADSUTIL, you can find more information here:
http://blogs.msdn.com/david.wang/archive/2007/12/12/howto-create-custom-application-pool-by-commandline.aspx
To do this in Nant you can use the exec task.
How are you planning on deploying your application?  Do you need this just for local installation?  There may be a better solution if you can give us some more details.