Best practice for a completely custom navigation?

If you want to keep some of the standard salesforce pages that deliver good value (like profile) you can add custom links to your navigation and include the url parameter “&isdtp=vw” to the end.  So this

url  /_ui/core/userprofile/UserProfilePage?tab=sfdc.ProfilePlatformFeed&isdtp=vw 

Will bring the user profile page without any sf header.  Not perfect,  but better.