Wahlie,
There's so much to cover here, and you could spend a lifetime finding the answer to this question. That's why gun nuts have so many guns. They have to find out the answer(s) for themselves.
I would say this...you're going to have more than one pistol. One or two will be tackdrivers for the range, one or two might be fun plinkers (.22's), one or two might be just for hunting (usually, these are revolvers in .357 or .44 mag), one or two or three or four or five or six might be investments/collectors items! Lastly, you'll have a few favorites that you will just come to trust to defend your life with.
As far as the latter, I would just use this as a guiding princple. Don't overanalyze. Pick a gun in a COMMERCIALLY LOADED caliber you're most comfortable shooting ACCURATELY (never carry handloads for self-defense, you're risking a lawsuit). That same gun has to be comfortable in your concealed carry holster in winter, spring, summer, and fall. Where you carry it is and what conditions that gun will encounter is also something to consider. One wouldn't carry a tricked out competition 1911 to the beach where it might choke on sand and saltwater, but one might take a Glock or an HK there. If one is in a setting that is not as hostile environment-wise, then sure, go ahead and carry your custom Wilson Combat 1911 that you just plunked down $5,000 for.
As far as common defense calibers go, they start at 9 mm parabellum and include .38 special/.357 magnum, .38 super, .357 Sig , .40 S&W, .45 ACP, .45 GAP and 10 MM.
You'll see more offerings in the popular and established .38/.357 mag, 9mm, .40 S&W, .44 mag and .45 ACP calibers. I suggest you start here and see what you are most comfortable with. Personally, I think the .357 mag and .44 mags are too much for the average shooter to handle in a defensive situation. If you believe Mas Ayoob, the .45 ACP in a 1911 is an expert's-only weapon, and you really need to train with it to get the most out of it. Starting with a 9mm is a good place for most people. I wouldn't go below .380 ACP (9mm kurz).
As long as a round doesn't over penetrate, I don't get too wrapped up in looking at terminal ballistics. Shot placement is equally important, and so that should really be what you should be focusing on. Also, you should practice with the ammo you intend to carry with, to make sure it cycles properly through your weapon.
I'll dig through some of my LFI notes on preferred commercially available loads. In the meantime, there is a kewl site to browse if you want to look at defense ammo.
http://www.ammolab.com
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