D9 is definitely in my top 3. Hard to say if it beats matrix. Matrix was earlier in the tech, and they did amazing things with it. The philosophy was interesting too. Though I understand most people didn't get it. My main problem with the matrix was that humans were used as batteries which would be completely inefficient. Almost enough to make it fantasy instead of scifi. But if the machines had some code in their that made them less likely to destroy their makers it'd make perfect sense. So I just pretend that its so in the movies and they never mentioned it
Otherwise, Avatar would be way up there too. Again many people liked the visual effects but were confused by the "military" tactics (they were mercs not military, and they were under the rule of a corporation). That plus the fact that space travel is expensive the more mass you move makes it make sense. So in my opinion it was scifi not fantasy.
I thought 5th element was late 90s...hmmm. Tough call for top 3. It was good but closer to fantasy than scifi so I'd have to boot it if I'm limited to top 3. Matrix, District 9, Avatar.
Edit: not that'd it'd be in my top three, but its often over looked. Pandorum is a great scifi.