If anybody's interested, here's how I care for my shell cordovan boots (Carmina 80184s in saddle shell) that I've regularly worn in the rain for the past two months, with photos of what they look like after each stage (cross-posted from http://www.styleforum.net/t/277505/epaulet-x-carmina-mto-group-buy-for-spring-2012 with some edits).
Caveat: I'm not an expert by any means. This is just what I do. I've both read and watched many resources, however, and it seems to have been working well at least in the short-term.
The materials I use are: a soft cloth, a deer polishing bone, a soft horsehair brush, and Renovateur. I wear nitrile gloves both when using the deer bone because it makes my hand smell weird and when applying the Renovateur because I don't want to absorb it through my skin.
1) Clean! I start by gently wiping them off with a dry, soft cloth to remove any dust or other particulate. Then with moderate pressure I wipe them down with a slightly damp cloth to clean them off. I find that this removes nearly all of the spotting from being in the rain (which is relatively minor to begin with). I give them a very quick brush at this point, too, just for kicks. Here's a photo of my boots just after cleaning and brushing with all of my supplies except the soft cloth:
2) After cleaning, I bone the entire boot. Some people suggest moving the bone in small circles, and I've seen others move it perpendicular to its long edge. But because of my particular bone's shape and a few rough spots that can (and have!) left minor scuffs, I mostly move it back and forth like a bow, using moderate pressure. It leaves behind a fatty, oily residue that conditions the leather.
Speaking of scuffs, here's proof that they can be smoothed like magic out by doing the above, before and after:
The boot on the right (below) has had the deer polishing bone applied to it. It's somewhat hard to tell from the photograph, but it has a waxier appearance at this point.
3) After boning, I brush the boots with a horsehair brush to flatten the oils left behind on the leather from the deer polishing bone. I imagine that the friction from the brushing warms up the leather and oils, helping the leather incorporate its nourishment---but I don't know whether this is accurate. The boot on the right has been brushed, the left has only been boned.
4) Next I apply Renovateur with a soft cloth over my index and middle fingers (too impatient to use just my index finger) in small circular movements. It soaks right in and darkens the leather. At this point any remaining water spots are gone. The right boot has Renovateur applied to it, so the leather is much duller than the boot on the left, which was just brushed.
5) Then I brush them again! I don't spend too much time on this, because I find buffing with a soft cloth has a much greater effect. Brushed on the right, Renovateur on the left.
6) After brushing, the final step is buffing with a soft cloth. If I had an even finer cloth (or nylon stockings or a lambswool shine mitt, neither of which I've yet tried), I think I could bring out an even greater shine with not much more effort. The right boot has been buffed, the left just brushed.
And the finished boots, radiating in diffuse outdoor light.