Long term running of an Arduino (years)

Surely I'm not the first one to think of this!

No there was a thread less than a year ago, search for that.

The arduino and the Basic stamp are like apple and oranges

Not as regards this issue they are both grapes.

Pretty much the same with any electronics, to be honest

Very true, note that as a rule of thumb for every 10 degrees C hotter electronics run the lifetime half's.

major risk is the spoilage of some kinds of capacitors, but you're talking ten years or so

Not quite true, depending on the temperature you could be talking about two years. (Running at 80C) But the failure of a capacitor is defined as the loss of capacitance of 20% and an increase in the ESR (effective serial resistance).

If your looking to make inputs robust then see:-
http://www.thebox.myzen.co.uk/Tutorial/Protection.html