Telerik has a great whitepaper laying out how to use their r.a.d. controls in SharePoint 2007. It’s one of the better whitepapers I’ve seen and covers everything from where various files go to creating manifest.xml files and wrapping up deployment packages via WSP file creation in build scripts. (I wish they would have taken the next step and showed using build targets to actually deploy onto the server with stsadm, but this is minor quibbling.)
I used Telerik’s radTreeView in a project earlier this year and loved its quick flexibility. Third party contols sometimes bloat pagesize, but I think that project saw an increase of 125K or so, which for our implementation was just fine.
Check out the whitepaper even if you’re not looking to use Telerik’s controls. There’s a lot of good info therein on general SharePoint development.