As said, it depends.
Diesels make so much torque because they're hideously oversquare. An engine that is undersquare (bore < stroke) will invariably make more torque than an engine that is oversquare (bore > stroke) of the same displacement - simply due to compression. The higher compression also contributes to more compleat combustion - and increased NOx, if left unchecked (which starts wandering heavily into theory in short order...)
How do you plan to drive? If you want stump-pulling low-end torque, you want for the stroke to be greater than the bore, and (ideally) you want to have the longest connecting rod that the engine combination will support (this increases TDC dwell time, which serves to maximise the use of peak pressures.) If you want to wind up the engine nice and tight, you'll want the stroke to be less than the bore - so you can "run high" while minimising strain on the reciprocating assembly (why do you think Diesels typically have redlines down around 2800-3000rpm, at least for the larger ones? There's a good reason for that - and for why the larger Diesels have things like twelve-speed transmissions bolted to their backsides...)
A "square" (bore = stroke) engine is a compromise between the two, natch, and that's why it's so wildly popular (I'd have to check, but I think the Ford and Chevvy ~400ci engines are both "square" at 4.000x4.000. Maybe the Chrysler 400 as well - but I'd have to check my notes on that. The Chevvy 265 might also have been square at 3.480x3.480 - again, I need to check my notes on that.) Compromise isn't always a bad thing - but there's a reason that dedicated racing engines can wind up to 10,000rpm all day without ill effects - and that's mainly because the stroke is down around 2.5" or so. (a V8 displacing 180-195ci is fairly typical I think - again, I'd have to check. It's late, and my head hurts.) Racing engines tend to be grossly undersquare, since they're mainly after high-rpm horsepower output. Truck engines lean more toward being oversquare (think the AMC258, used in Jeeps for years - 3.750" bore x 3.895" stroke) to maximise low-rpm torque output. This means lower redlines as well (even the typical stroker is mildly undersquare - 3.875" bore x 3.895" stroke. This reverses if the block is bored out .030" or more - 3.905/3.935 x 3.895, then. But, it's not enough to cause great difficulty, and the increase in compression still helps low-speed torque output.)