The guys who run Astronomi-con have a little store thing on the side, and they offer a CD with 50+ tournament proven special scenarios complete with table layouts, special rules and (I'm pretty sure) photos of the actual tables for reference, plus their own set of Apocalypse-style rules (put together long before Apocalypse came into being) and selected photos from the various Astro events. It's $20 plus $5 shipping, but well worth it, IMHO - these scenarios are really awesome to play, and they're about as far from the same tired old "kill everything" style missions as you're ever going to get! And even better, these scenarios have been proven to play well even with Flyers, VDR creations, special characters and oddball niche armies running amok on the table!
www.astronomi-con.com
You might try contacting them to see if they'll show you some sample missions to see what it's all about before you decide to buy it or not.
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Link - Warhammer 40k Special Scenarios
I saw this post over at the Librarium-Online.com forums. The original poster was asking for special scenarios and I saw this reply posted by Wraith and thought I would share it -