I'm leaving on a bike trip fairly soon, and I have a choice between two bicycles. One's a 21-speed mountain bike with Shimano shifters and eyelets (relevant for a national tour). Its downside is that it's too small for me -- the frame, that is. I have the seat jacked ludicrously high, but it works.
The other bike's a road bike that is my size, but needs a total rehaul. That is, it's in excellent condition, but I need to upgrade from its current 14-speed to a 21-100 inch gear range, replace its handlebars, try to fit 700x35c tires on it, and fasten false eyelets for a rear rack. I also need to move the shifters up from the (stem?) to the handlebars. It'll cost hundreds.
My question is, would I be as well off taking the bike with the smaller frame? Not even weighing in the costs of overhauling the road bike, does size make a difference in riding quality for long tours?
So it sounds like you're doing some loaded touring? If that's the case, you're going to want the bike that's most comfortable for you to ride long distances. If the mountain bike is too small for you, it likely isn't comfortable, eh? If it is comfortable, go for it! Old, rigid-fork mountain bikes make good tourers. You may want to at least add some bar ends so you can get more hand positions.
It sounds like your road bike may be pretty old, and will probably cost lots of money to convert into a somewhat viable touring bike. Even then, you may find that the geometry is less than ideal for operating with panniers attached (especially on the rear -- you may find that with the short chainstays, your heels hit the panniers.) Have you considered purchasing a purpose-built touring bike? The REI Radonee and Fuji Touring are both relatively inexpensive options you may want to consider; it will probably end up costing you nearly as much to upgrade the road bike as it would to purchase a new bike. Buying a used tourer is also an option, but they're not that easy to come by in most places.