Shaken and Stirred, Java style

Finally, after much searching, I've found a guide to the amazing boat chase that starts off The World is Not Enough, the best of the modern Bond era:

Continue east along the dockside and then turn right following the signs to South Quay DLR station. When you get to the station, cross over the road to reach Millwall Inner Dock. This is the scene of much of the amazing boat chase in the opening sequence of the James Bond film The World is Not Enough (1999). James Bond (Pierce Brosnan), in his jet-boat, is chasing the Cigar Girl, an assassin played by Maria Grazia Cucinotta, in her Sunseeker powerboat.

Walking about 200m along the eastern dock-side you reach the old London Arena site, and a floating Chinese restaurant. The dock was the scene for the stunt where Bond jumps over a stationary boat, corkscrews through the air and knocks the machine gun off the back of the Cigar Girl’s boat.

A little further along, you will reach the Glengall lifting bridge. This bridge was used for another clever stunt – the Cigar Girl notices that the bridge is closing and speeds underneath, so as Bond reaches it he is too late to get under. He spots a lever marked “dive” in his boat and pulls it, the boat disappears under the bridge and pops back to the surface on the other side. In typical Bond fashion he takes time to straighten his tie while underwater.

For continuity geeks, the route of the boat chase is an odd one – it starts at Vauxhall Cross, the HQ of the real MI5, and within a minute reaches Tower Bridge (in reality this would take at least 5 minutes even for a jet boat). Then they turn south into Java Wharf, which is a dead end off the Thames in Southwark just east of Tower Bridge.

Luckily, by the magic of film, this gets them here to Millwall Inner dock on the Isle of Dogs – in reality another dead end. There is then a gas bottle explosion which is actually in the Blackwall Basin just east of Canary Wharf.

His route blocked by the explosion, Bond appears to be back on the River Thames west of Canary Wharf pier – his on-board computer is offering him two alternative routes using either the North or South Docks to speed through the Isle of Dogs. In fact, Bond's route takes him through Wapping (a mile west), Billingsgate Market and through
the Royals. He pops up onto land and drives through the market using his boat’s jet engines for power. Then he appears to pop out of a restaurant window at Trinity Buoy Wharf and back into the Thames in time to catch the Cigar Girl and force her boat
aground at the Dome.

And now, of course, the chase itself:

And just for fun, the ski chase too: