Johan, as far as I know, you can't upgrade just a site; you can only upgrade your whole server, or upgrade a content database at the time that you attach it. (See Arpan's blog entry: http://blogs.msdn.com/b/arpans/archive/2009/12/29/upgrading-to-sharepoint-2010.aspx)  That means that you basically have two options that I can see, which is along the lines of what you're saying:

- move just the list data you want into a fresh site collection in a fresh content database, and then upgrade that content database. (If the amount of data you're working with is small, writing a script is easy. If not, you can buy third party tools to move, back up, and restore list data.)
- install a fresh install of SharePoint 2010 and write a script that migrates content between the two.

Keep in mind with the latter option, you need to manually configure the lists, etc., so they mirror what you had in the old environment, unless you programmatically copy their definition and recreate them programmatically in the new environment. I would suggest simply moving the data and then upgrading the site collection, so you don't need to recreate the lists.