Step 1: TripAdvisor
First we hit up TripAdvisor and check out their "Things to Do" section.
Step 2: Google Maps
Then we map out everything we want to see and do on a shared Google Map, so we can start grouping things that are close together.
Step 3: Google Docs
Next, we create a shared Google Doc, start listing the attractions, and figuring out which day to do what. Once we start booking flights, trains, hostels, etc., all the times and confirmations numbers go here.
Step 4: Mobile phone/apps
For this trip, I've used the Labs feature in Android Google Maps to download all of London for offline use, in case I don't have a mobile signal. I've also installed two different apps that give live train and tube schedules.
Step 5: Paper
As great as technology is, it's not quite perfect. Laptops and phones can break or run out of battery power. Before we leave, we always print out a few copies of our most important information, just in case we can't access it electronically.
Just remember that steps 1-3 do take a while, and you'll often come back and update them as you get advice from people on what to see, or realize that you've scheduled way too many things for one day :)
Hope this helps. Happy travels!