I've always wandered around with notepad and pen, just in case an idea pops into my head, or I see something worth jotting down (or the ISBN of a book that I would prefer to check out online). These days I do the same thing with my cell phone, and I often take pictures of funny/interesting things I see (I try not to take pictures of people if I can avoid it - people sometimes get funny if a stranger randomly takes a picture of them...). Some of these make it to backdrops, NPCs, etc.
When I was writing adventures/scenarios for my weekly (or whatever) game, I would look at the strengths and weaknesses of the PCs, flick through the rule books, and look at the adventure types. Sometimes just going through the types of runs was enough to flesh out a story - I hadn't used Critters before in an adventure, and I was reading through one of the SR2/3 books that used to outline the types of runs and payments and so forth, and came up with a scenario that used a cave system as the backdrop (one that the players were familiar with in the here-and-now), some natural hazards, corp security and a kick ass Critter. The ideas pretty much just came together, and the whole thing wrote itself (more or less).
If you choose to balance runs for your team, it's not hard to pick a formula, pick the opposition (based on the PCs) and go from there. At the end of the day, I guess it comes down to practice, practice, practice...