I saw 2 of 'em: once in a game I'm still playing, fielded by Ragnar (mostly horse archers and a few Berserkers--this is medieval era but I slingshotted from Liberalism to Nationalism, researched Mil Trad, and how have Cavalry, although not many are built yet and there's a city I've captured, re-lost, and recaptured something like 4 times already, due to his massive reconquest stacks), and once by Montezuma when I'd taken a few of Catherine's cities, and unbelievably she went from bad relations with Monty to volunteering to be his vassal if he'd declare war on me (went from Friendly to war with the snap of a finger--NEVER TRUST THE FREAKING "ATTITUDE" THEY PRETEND TO HAVE TOWARDS YOU!!!) I had tanks and infantry, but three different stacks of Cavs and Cannons came at one city: a 75, a 45, and a 25. Unbelievably I was able to hang onto the city by airlifting (this was overseas from my original land mass) Marine units promoted to CG2, each turn, to supplement my original 15-deep attack stack of tanks, cannons (hadn't gotten Artillery yet), and infantry. Lost about half my units, but the city held, and when Monty was down to about 20 units total, weakened to about 1 point each, they finally gave up and ran back to his zone.
I've also seen runners-up obsolete stacks fielded by Cyrus, of all people. And one time, oddly, by a Churchill AI (which completely caught me off-guard!)
To me it's a matter of the military situation. If I can prevail eventually in the war, my knee-jerk is to keep. In fact, the only plundering I like to do is to wear Towns down to Cottages (and let them re-grow to Towns after my cities work the squares). The two challenges to that approach are cultural and military: it eats up more units to occupy the conquered and kept cities; and if the enemy culture is strong nearby, the cities spend most of their time in revolt over and over until they go back into enemy control.
If I'm militarily weakened and losing the war, I grudgingly go into "sore loser" mode and just plunder and raze everything in the path of my units--even to the degree of avoiding combat, just go for plunder and razing.
Not in regular Civ4 or Warlords (not sure about BTS rules on this). A well will destroy the fort, and vice-versa. However, if a city gets built on a resource square, it works the resource as if it had the well/plantation/mine/whatever just outside its fat cross.