Question: Some years ago, I picked up a Cannondale R3000 and moved all the components to my current bike as an exercise in bike building, never repeated (in fairness, the Cannondale fit me a little better but my beautiful 1998 Klein has such a sweet, sweet paint job...). I've been putting the frame on Craigslist off and on for a few years, but no one seems to want to pay what I'm asking. Regardless, my current MTB is an all-mountain beast that I bought before I knew my riding style, and I'm thinking of picking up a more cross-country steed.

Times being tight and all, is there anything preventing me from building out the Cannondale road frame as a mountain bike? Obvious [potential] answers (e.g., tire clearance) are good, more involved ones (e.g., frame robustness) are too. I'm trying to get a picture of what might lie ahead in this venture.

Answer: 
If you want to use it for "proper mountain biking" (however you define that) the answer is almost certainly no. You won't be able to fit wide enough tyres to give you decent grip, and punctures are likely to be a problem. Additionally, the geometry will be all wrong (if you put straight bars on it you'll probably feel quite cramped without a long stem, which will make the handling wierd). That's without getting into the strength issue - Cannondales have always seemed quite fragile to me (but that's an opinion only, never owned one).

However, if you want something for blasting along relatively smooth forest trails that aren't muddy, fit the widest grippiest tyres you can and give it a whirl. Despite what I said about strength in relation to proper mountain biking, road bikes are surprisingly strong provided the forces are applied to them in the way the bike is designed. A few small bumps are unlikely to break it assuming you're not a large rider, you don't try jumping and you don't crash. It'll be a very different experience from a proper mountain bike, but on the right trails could still be a lot of fun.

Ultimately though for proper cross country mountain biking you do need a mountain bike (or a cyclo cross bike). I'd suggest trying ebay with a reserve price to find out what people are prepared to pay for it. Second hand aluminium road bike frames aren't that desireable any more, even if they did have dura ace on them when purchased, simply because carbon frames are so much cheaper. However, second hand mountain bike frames are also pretty cheap, and a couple of hundred dollars towards one from selling the R3000 frame is infinitely more than nothing if it's just gathering dust.

Hope this helps.
Converting to a straight-up mountain bike would be hard. Converting a road bike to a 650B bike capable of handling dirt trails and gravel is a pretty established practice, mostly entailing swapping the wheelset and brakes:
<http://www.cyclofiend.com/cc/2010/cc769-joehuddleston0410.html>
It's more usually done on older frames, but nothing necessarily precludes doing it on a newish racy frame. However, a narrow chainstay/seatstay/fork gap may make fitting fat tires difficult.

However, you'd be able to pick up a decent used mountain bike for the price of a decent 650b wheelset, especially if you'd be fine with a rigid bike. $125 or so can get you Tange Prestige with early 90s Deore LX and the like.

If you want a project for your R300 frame rather than selling it cheap, there's always a singlespeed conversion (the Wabi wheelset is great for the price).