For automotive engines running at higher rpm, with one spark plug per cylinder as was the norm, a bore of about 4" or 100 mm is the limit for complete fuel combustion during the power stroke. With a few engineering tricks, some big-block V-8s went a little larger, but those engines were fuel hogs. Example: the Chevrolet 454 had a bore of 4.25". In street engines since World War II, few auto engines have gone much above 4".
Yes, there are few modern exceptions, including the 6.4L HEMI, which has a 4.09" bore. I know you will say it has dual ignition, which it does, but the reason for that is the combustion chamber design, which is why its smaller bore sibling also has it, which is necessary for those engines on order to achieve acceptable emissions.
Historically, one of the reasons for the larger bores was to decrease valve shrouding on 2V wedge/quench chamber designs. Engines like the Chevy 305 were limited in valve size, and subsequently head flow, due to this. The aforementioned 454 (like the Ford Cleveland) used canted valve heads to improve flow even further. With a hemispherical chamber, shrouding is less of an issue, same with pent-roof, which had a tendency to be fitted with multiple valves for intake and exhaust to improve flow, reduce valvetrain weight/spring pressure and increase efficiency.
With a pent roof design, bore size became much less important, which is why most SOHC and DOHC mills have smaller bores. They are more efficient, less swept ring area and still able to move plenty of air.
To be able to rev, larger engines have to limit stroke. They should be oversquare, meaning the bore is larger than the stroke. For low-speed torque in a lower-revving engine, a longer stroke is better. Most small four-cylinders are undersquare, meaning the stroke is larger than the bore.
Of course worth mentioning is that many of these small four cylinder engines can really rev, like Honda's S2000 engine, which of course spun to the moon, was originally almost square, and then became slightly undersquare:
F20C: 87mm bore, 84mm stroke
F21C: 87mm bore, 90.7mm stroke
Ford's Modular is another thats very close to square in some configurations with the reasonably rev-happy 4.6L DOHC mill being 3.552" bore, 3.543" stroke, the 5.0L Coyote being 3.63" bore, 3.65" stroke (slightly undersquare), while the flat-plane Voodoo engine is 3.70" bore, 3.66" stroke (slightly oversquare).
On the other end of the spectrum, the old Windsor engines like the 302 were quite oversquare with that particular engine having a 4.0" bore, 3.0" stroke.
Of course there are exceptions (even if we are just talking exclusively racing). The huge Pro Stock Mountain Motor engines are over 800ci. The Kaase Ford mill for example achieves 830ci with a 4.77" bore and 5.8" stroke (quite undersquare) and these rev quite high.
For a given displacement, with the above limitations in mind, fewer cylinders are better because of friction loss through rings and gearings. Given a choice between a 5.0 liter straight-6 and a 5.0-liter V-8, the six will be a better choice for economy. When the bore exceeds the magic 4" limit, though, it's time to go to more cylinders.
While the 8 can be more oversquare and will tend to make more power, which is why BMW bumped up to a V8, and later V10 in the M5 and M6 cars (both 5.0L) from the base I6's, even though they had some very capable (but smaller displacement I6's in cars like the M3.
Certain engine configurations cannot be completely balanced. These include any configuration with fewer than 6 cylinders. An inline-4, as mentioned, can have primary balance, but secondary imbalances cannot be eliminated, and the same is true for boxer-4s. An inline-6 is ideal, and for years Rolls-Royce used this type of engine. It isn't coincidence that the Chevrolet, Ford, and Chrysler I-6 engines are among those automakers' best and most durable.
Yes, and another thing worth mentioning is that these I6 engines also have more mains/crank journals. The Ford 300 I6 had 7 whereas your typical V8 has 5.
A 90° V-8 has primary balance with only a minor secondary imbalance. A 60° or 120° V-12 is another ideal configuration. A V-6 has significant secondary imbalances. All of this is a gross simplification, so please don't shoot the messenger. The recent Ford 6.8-liter and Dodge 8.0-liter V-10s ideally should have been 72°, but were 90° to be able to use existing tooling, and tricks were required to balance these engines.
Huge slow-running diesels don't have to worry about a lot of these factors. A gigantic 2-stroke diesel propelling a ship is running at only a few hundred rpm at most.
Hope this helps the OP.
Very well articulated!