DS,
I am in the boat as you!  The way I see it there are 3 real options.
Let me first say, I don't like the building a deck on top at all.  And if I were you, I'd stay far far far away from that idea.  Load-issues aside, it isn't a good idea... there are too many variables that can go wrong with the roof, and now you're stuck with a deck on top of the part that is sealed.  Most people in my area have opted for the first of my options.
1) Hard Fiberglass roofing -- this is akin to having a boat-hull material (resin, woven, etc.) built as the roof.  When done properly it will last 50+ years, and you can dance, jump and walk on it as much as you want.  It is also the most expensive.  It is also the most problematic if it isn't done properly.  You want to keep from being talked into a surface mount rail (and they WILL try to talk you into it) -- you want a FACIA mount rail system... you DO NOT want the penetrations of the rail posts to go through the roof.  I have some quotes for this if you need more info, let me know.
2) This stuff: 
http://www.amesresearch.com/sd_app_article.htm
I have not done it, but I have been VERY curious about it... it seems too good to be true, but who knows.
3) The single giant sheet of rubber that wraps down and over the edge of the surface... this is basically a flexible version of #1... cheaper and more DIY... I don't know enough about it, but it would be very nice -- I see it in JLC and FHB all the time...
Hope this all helps -- I have a mutt-mix roofing on my flat deck-roof... and I haven't painted it in a few years... and it looks like it.  No leaks... but I'm living on borrowed time.
Pete