My starting points usually involve cultures/races/situations and their interactions. Once I have a general idea of the cultures, I think about what type of geography and climate is best suited to them and start mapping from there. Sometimes I'll have an idea about some unique or odd geographical feature (like a huge archipelago or a massive impassable mountain range), and I'll throw that in at an early stage, maybe even start the map with that feature and build out from it.

I'm not an authenticist when it comes to plate tectonics, etc. I try to hold true to actual physical principles, but being super nit-picky takes a lot of the fun out of it for me. Not that there's anything wrong with being exacting as far as your realistic-ness goes, it's just not how I roll.

In the end, it comes down to what feels right for YOU. My advice is to try creating worlds in a variety of ways and see which sticks for you. You can go extreme-top-down, i.e. creating a solar system-->planet-->geology/geologic history/plate tectonics-->weather/climate--> etc, etc, etc, or you can go the opposite way, starting with a single city or kingdom and building up from there, or some combinations of the two (that's where I tend to fall most of the time).

That link that Amber provided is full of great info, and I've found this and this and this to be useful.