Generally, the mechanical efficiency in a racing engine, where higher crank speeds are not a problem, is better with a larger bore and smaller stroke. The short stroke results in less frictional loss since speed is considerably reduced. The breathing ability for a given cylinder displacement should be increased with a larger bore because there is simply more area across the bore in which to fit the larger valves. The shorter stroke will also allow relatively shorter rods and a shorter block deck height. All of this adds up to reduced engine weight. Of course, this is a complex technicaly consideration since it is possible to have the rod ratio too high for the displacement, resulting in induction feeding difficulties. This is a matter of balance and design skill.
Now stroke length versus performance is always a flame war. The common factory sbc lengths are: 3", 3.25", 3.48" and 3.75" (good luck tryin to find that 3.1" crank, they're still out there though

) In low speed engines (ex: street driven), there is some degree of performance gain with every increase in stroke, all the way through 3.75". There is not however, a linear increase in output (power per inch) as the stroke goes up. There maybe be more torque; and with considerable work, it is possible to attain a pretty good specific power curve up to a stroke of 3.48".
When maximum specific power is desired for racing purposes, other considerations enter the picture. In this instance, the stroke length must be dealt with in terms of the available rod length and piston design. These are important factors in the induction efficiency of the engine; after all, this is where the game is won or lost. In simplest terms, the reciprocating piston, internal combustion engine can be viewed as a pump. The better it draws in combustible gases, burns them, turns the crank and pumps them out, the more power it will produce (simple right?). Now considering those requirements, it is possible to gain a fairly decent rod length to stroke ratio at any stroke lengths between 3" and 3.48" (sorry 383 and 400 guys

). When the restrictions of piston design and induction system design enter the picture, the best compromise is the 3.25" stroke (of course any of the common strokes can produce suitable power curves if the overall engine is properly designed).
An engine with a stroke of 3" should have a relatively high specific power curve through a wide engine speed range. However, with a stock length 5.7" rod, the piston compression height is very tall. With all this room between the pin and the piston deck, the piston is very heavy. A longer rod would put the pin higher in the piston and save some weight. This is a slight secondary consideration and one of the possible advantages of longer strokes.
A stroke length of 3.25" provides an excellent compromise. The rod length can be nearly optimized without severly restricting the piston design. A 3.25" stroke has an optimized rod length of 5.9" (a 1.8:1 ratio). This rod is only slightly longer than the stock 5.7" rod.
With the 3.48" stroke, the piston design becomes a problem because of the high pin placement. Above this engine size/stroke length/rod length, the peak power curve falls off rapidly beyond 8000rpm (does anyone on this site have a 8000k 350?) A lot of circle track 350's are running 5.85" rods (1.7:1 ratio), but many Nascar 350's are using 6.0" rods. 5.7" rod engines don't have th same fuel specific curve as the short rod engines but are almost as good in output. The longer rod engines with smaller volume, 4bbl intakes seem to be more flexible and produce a broader torque peak, which would work quite well on the street.
So after my novel, I'd say the absolute optimum engine is the 327 with 5.9" because of the fuel specific curves you can create with it. On the other hand, I imagine most people who are interested in what they should run for bore/stroke are mainly driving their engines on the street and not building for 6000 plus rpms so they should not worry about bores and strokes; in which case:
There's no replacement for displacement.