There are many excellent posts on the 'pedial extremity' topic lately, coming from blogs like Cold Thistle http://coldthistle.blogspot.com/2011/07/your-feet.html, covering everything from socks to insoles to climbing boots to skiing. I don't think I can hope to obsess quite so much as Dane does, but there seems to me to be a place for the less rare air beginners out there. In particular, I used up a bit of my foot karma early on, squeezing into La Sportiva Mega's which were not only shaped nothing like any foot I've ever seen, but about 2 sizes too small. Which is what you get for taking advice from climbers who have only barely survived themselves.
In my later years I've started to see feet/knees/back as the key continuum of good health for hikers, climbers and skiers, and have a few things I'd like to have done better earlier. One is wear only shoes that fit, as opposed to those which look good. This is a bit of a challenge for those of us with any aspirations towards fashion, and I know my brother for one has had a pair of NF trainers banned from the home for offending the fashion police (they look fine to me, but other sources agree with the enforcer, his wife.) I've only had one really good boot fitting (thanks to Jan Wellford of the Mountaineer,) and it's something I would have done much sooner if I knew how positive the results would be. I tried on shells with a blind eye to what looked good, and went for a relatively old design (Garmont Mega Ride), because it fit my relatively low volume foot. Given the recent developments in very light boots, and the expansion of these into climb and ski setups, I may revisit soon, but taking the time to sit with a good fitter (and it takes more than an hour) is well worth your while. I've also been using orthopedic insoles for years now, both off-the shelf and custom, and am convinced these make a great difference too.
That said, there are lower cost alternatives to a full custom approach (my boots were on sale, and the custom fit cost nothing extra.) Spenco makes excellent insoles and they are definitely better than stock ones. Companies like Sole (http://www.yoursole.com/) make a good alternative too, and one you can bake to shape in your oven, as well as comfortable if pricey flip flops. My first mountain boots, the weight training Galibier Super Guides, were not much fun without the neoprene insole I used to defray the cold conducted by crampons. Those boots (bought 30 years ago) are still in use by my long-time climbing partner, and while heavy, are a great example of old-time craftsmanship. If you have a chance to demo boots jump on it, because I cannot say for shame how much money I've spent on boots which did not really fit over the years. I even wore a lovely pair of Scarpas for years before admitting it was probably causing the annual loss of a big toenail, not to mention a bit of frost nip. If you can find a brand, or even insole/sock combination which works for you, go with it. My longest-standing boots are hiking boots from Technica, sold to me used for $90 by the generous Rich Gottlieb of Rock and Snow, still going great guns even when I'm not.