Just be meticulous, but smooth. Everything in your bag should have a place, it comes from there, and goes back there as soon as is feasibly possible... once you're used to the system it becomes second nature and stuff just...doesn't go missing...and if it does then you know that you've got a problem right away, rather than 'oh its probably just in the bottom of the bag'.
Some kits in industry etc will be in a flight case with the normal foam cutouts, and a red sheet below all the items, so you can very quickly see at a glance, if there's any red, there's something missing.
Lens caps are a bad offender...I don't use them, hoods don't take up much room to have out in my bag and make for quicker access, but the best thing to do is just ALWAYS put them in one pocket... left back pocket or similar is usually free, means that again, it's always either on the lens or there.
and there's nothing you can do to stop stofens constantly going missing, I buy them like, 5 at a time... >_>