One of the most controversial subjects in motorsports is that of proper engine break-in. It ranks right up there with Global Warming.
I've broken in 3 motorcycle engines, 1 quad engine (working on my second quad as of this writing), two car engines and 3 truck engines, including a 4 banger Toyota, a 6.0 liter Vortec engine and a 6.6 liter diesel engine.
All of them run exceptionally well except the very first one I did, a Yamaha FZR600 sport bike, which I broke in according to the manufacturer's owner's manual. My brother bought the same bike at the same time, and we broke them in together, using the same technique.
Both of the FZRs were weak in power compared to other bikes, both had flat spots at just under 6,000 and made nasty noise at 7,500rpm, (Red line was around 10k if I recall.) The flat spots were at the RPMs that we didn't go above until recommended by the mfg. (We exceeded the 5,500rpm mfg suggested limit at 300 miles and the 7,500rpm limit at 600 miles.)
Following is the method I used in the past (and am currently using on my new quad) to break in the engines.
Warm the engine up completely. Load the engine by opening and closing the throttle hard in as many gears as possible, alternating between short bursts of hard acceleration and deceleration. Shut it off and let it cool. Check things out, loose nuts, oil etc.
Change your oil after the first hour or two of operation of the engine. That's when most of the burrs (small metal shavings) are taken off, and you dont' want that metal seating itself in the other components of the engine.
Warming up the engine completely is extremely important, even AFTER the break in period, especially if you're going to ride it hard.
There are a few good articles out there explaining why to break in your engines using this method instead of the baby it method. A very good article that explains the mechanics of how the engine break-in works can be found here.
Anyone familiar with machining metal and/or the physics of engines should quickly understand why breaking it in hard is very important for performance, power and reducing engine trouble through-out the life of the engine.