I've been using a Yakima rack on my G&K imported 2006 Smart ForTwo Passion (glass roof) for ~8 months, and have been very happy with it.
It was installed by RackAttack in Portland OR, and these guys already had installation instructions (including which clips were needed, etc...) in their internal database. Though one source for me was ClubSmartCar.com (search their site for "Roof-top Yakima Rack").
In summary, use #34 Q-Clips, and make sure its installed TIGHT, and I mean so tight that when a 200lb guy yanks on them, they don't even hint at budging. I went with the steelhead "fork mount" bike holder, and recall needing to sign a waiver - as the rack is not approved by Yakima or Smart. Speeds upwards of 80MPH were no issue, though I personally would avoid putting a box up there for anything above ~60MPH.