Well, I don't have any bias against a given cartridge but I've always been a 1911/45ACP kinda guy. For target shooting, I've fired many 1.5" to 2" groups at 25 yards from a couple of my 1911s including one completely bone stock Springfield Stainless Target model but keep in mind, I've shot this combo a LOT. With 9mms, I've shot a few groups around 3", maybe a bit smaller from various 9mms. With my Glock 23 and a 3.5# connector, I don't think I've ever shot a group smaller than about 4" or maybe a bit larger. I had an EAA Witness Silver Team (single actio nCZ75 type pistol) that I used a lot at 100 yards and fired several 8" groups with it but most were in the 10" range and that was using American Eagle ammo. This should translate back to 2" to 2.5" at 25 yards. In my experience, 9mms and 45ACPs are more accurate than 40S&Ws but in my experience, the gun, trigger and ammo has a lot more to do with it than just the cartridge.
For wounding or stopping ability, if we're limited to FMJ choices, I would feel better armed with a 45ACP shooting 230 Gr ball ammo than I would with a 9mm of some sort shooting 124/127 Gr ball ammo. Assuming that we're talking about modern expanding HPs and shooting them from guns that are very reliable with said ammo, I'd feel well armed with 115-127 Gr 9mm loads, 155-165 Gr 40S&W Loads and 200-230 Gr 45ACP loads. I like CorBons, Rangers and Gold Dots for 9mm, and Gold Dots, Golden Sabers and Rangers for 45ACP. Don't have a strong enough opinion of defensive 40S&W ammo to make a solid statement though I'd probably stay with Gold Dots and Rangers. I have relatively limited experience with the 10mm and the 357 Sig though if it was reliable and shooting any ammo of known reliablity, I'd feel very confident with either of them.
Just my opinion, but no one will convince me that a service sized pistol (4" barrel or larger) shooting any of the ammo combinations listed in the previous paragraph won't do a very decent job of slowing down any single bad guy in relatively short order. The most important thing to me in a SD pistol is that you have completely confidence in it. It should be at least 99.9% reliable and you should be able to clear a malfunction without thinking about it. You should be able to draw and put two rounds into any target within 10 yards in under three seconds and as a citizen (not LEO) you should think agressively... Two shots, everytime and move in closer... if the bad guy is still moving or talking, he gets two more shots faster than you can consciously access the situation.
That is more important than 'what cartridge' in my book.