SP Application Templates, Fixes, and the SP Template Project
Bil's been posting aplenty on the SharePoint Application Templates (the SPATs?), I'll play aggregator.
A comparison of the basic and custom versions of each
The Fixes for InfoPath
In addition to Bil's great tips on fixing the data connections and submit links, you'll find out fast that even the less complex forms need some help. You'll want to open each in design mode (Open the forms library, Modify settings and columns, Edit form) and then re-Publish back to the site to avoid the ".xsn not found" message.
The SharePoint Template Project on SourceForge