Wow,
I was browsing the MSDN blogs and came across this soapbox video: http://blogs.msdn.com/vsto/archive/2008/01/17/sharepoint-workflow-tools-video-interview-with-john-durant.aspx.
John Durant speaks about creating SharePoint workflows with Visual Studio 2008, but he also mentions there is going to be a powertools package.
One of the tools which will be in there is a tool to upgrade a Sharepoint Designer Workflow to a Visual Studio Workflow!
That's great news! That way you'll be able to add custom code to a IW generated workflow...or redistribute it using the feature and solution framework!
(I must see more of these videos ;-) )