Kimi,
Our main SFDC administrator, List specialist and myself just had a discussion on this. For us we're planning on the following:
1) Hide the inactive (dead and no longer in business or in the related industry) and those missing email address so it doesn't show up in Marketo.
2) Hide contact records by industry in SFDC whom we will never market to. (I'm hoping this will be an easy process)
3) Dedupe as much as you can in SFDC so those don't sync to Marketo. We're struggling with this one.
I wish we had done the above first before doing the integration.