I wing it every trip. =D

Of course, I'm a single traveller -- as abmj-jr mentions, reservations might be a good idea for 3 people. That being said, if you make reservations for a rough area, you can leave the details up in the air. I.e., reservations in Kyoto for a few days, then decide what to do (including day trips to other cities) later.

+1 for booking.com; I use both it and hotels.com.

What's this huge list of places you have? Maybe some of us here can help you narrow it down a bit, or at least point you into certain directions for planning but not planning too much.