Whether it's a complete world for a home-brewed campaign setting or a specific castle or set of ruins, sooner or later any GM that doesn't rely solely on modules is going to need to design a map.
So... how do you do it? Graph paper (hex or quad?), blank paper, computer tools (which ones?), just make it up as you go along? Do you have pre-designed "generic ruined temple #3" that you can pull out when you need it? Do you base on real-world maps?
When designing terrain, especially large regions, to what extent do you take into account geological plausibility? (i.e. jungles & deserts running into each other is pretty unlikely in the real world) If you do include something that is geologically unlikely, do you make sure to come up with a reason for it while doing your design, or wait until someone asks and make something up?
Do you design terrain first, and then add political boundaries, or do you start with the political boundaries and then define terrain around them?
Personally, I prefer computer tools because it's easier to just plop down a row of generic "mountain range" icons than to draw all of those little peaks, and it makes a nicer-looking map. I recently downloaded AutoMap, but I'm not 100% sure that's the tool I'll be staying with. I'm still working on the overall regional map, so I haven't got any of the individual locales set up, but I expect to try to get a few "generic" dungeon / ruin / castle maps designed so I can be ready for my group to go somewhere I hadn't expected.
I try for at least a modicum of geographic plausibility. I discovered the other night that I had a river starting less than 20 miles from the edge of the desert, and had to consider for a while if that was what I wanted to do. I think it's probably ok, I'm thinking about some physical, as well as magical, explainations (the desert is the result of some catastrophe in the distant past, for example, and the edge is clearly defined by the range of that catastrophe). Putting dense forest right there, though, wasn't going to work for me.
In this instance, I had an idea going in about how many political units I was wanting. I designed the terrain for the overall region, then scaled it so that it would reasonably hold 10-12 sub-regions, and finally set the boundaries for the sub-regions along natural lines (rivers, forest edges, etc) where I could, and where they made sense relative to that. I'd wanted the region to be geographically isolated from the rest of the world, but not an island, so I put a significant mountain range along about 1/3 of the border, and a large desert along another 1/3 or so, and made the rest coastline. I also limited the use of long-distance ships to another race entirely (not a terrain feature, so much as something I needed to keep in mind when designing the terrain -- ships give them SOME contact with others, but not enough that they (or I) will need to know anything about the geography of anywhere but this region any time soon).
Personally, I like D&D because I find OCD much more interesting than ADD.