Interested in how important this is to people. Not really colour schemes - more navigation. I have a couple of forums (one running off ezboard and another using vbulletin lite (currently developing with vb 2.0) and have a good level of consistency with colour and feel - and there are links back to the index page of the "parent" site - but no "real" navigation (as seen on Sitepointforums - but not on this subforum)
How important do peeps think it is to have "genuine" navigation, verses a "subsite" type model?
In my opinion, visitors might feel more comfortable if the navigation is consistent throughout your site.
Some visitors may be unfamiliar with bulletin boards such as UBB or vB and they might appreciate some consistency.
Taking sitepointforums as an example, the forums are definately defined as a separate subsite, with a separate layout and even (to some extent) different graphics. However, the navigation along the top is familiar to users of the other sitepoint sites.
My two cents.
I think it should be based on the situation. How much do you want your forums to be associated with your site? If you would put your forums into your site's layout, will it have too little space?
For my site/forums I'd use a customized navigation with the same colors. The forum would have the site's color, but would not be cramped into the design of the site.
I think it's important to tie things together and provide site navigation. I agree with MMJ that consistency is key - nothing annoys me more than ending up in a 'dead end'. In addition, if the forums are the heart of your community, then you want to provide 'arteries' for further site browsing out from the forums. Your forums will probably be visited more often than your front page, so it makes sense to provide links to other features from within the forum area.