I have an '03 5200. During the 3,500 miles I've put on this bike I've experienced a few creaks and rattles and have managed to eliminate all of them. Completely tight and quiet now.
specs:
60 cm Trek 5200
Look PP357 pedals
I'm 6'1" 205 lbs
sources of creaks and rattles:
Bike shoe cleats: make sure the cleats are screwed tight to the shoes and use dry silicone spray inside the front and rear lips of the cleats where they clip into the pedals (dont spray the bottom of the cleat where it contacts the pavement or you'll make them even more slippery to walk around in). just a little grit in the cleats can make a lot of noise. Sometimes on a long ride (like a century ride with many rest stops) I'll get grit in my cleats from walking around which causes another creaking noise. When this happens I give my cleats a hard squirt of water and this solves the problem for a while. The silicone spray works better and lasts longer than water though.
Chain: Boeshield T-9 drip lube (every 100 miles). I've tried MANY lubes and this one is by far the best. Boeing developed this lube/rust preventer for thier aircraft production. Then, several years ago, woodworkers discovered it for their shop tools (which is how I came across it). About 5 years ago I started using the T-9 spray on my bikes and noticed a few bike mechanics had also discovered it. Then Boeing got word of this and now markets a great little drip lube dispenser specifically for bicycles (much better application than the spray can). T-9 really quiets the chain down and improves shifting performance. It collects more dirt than the dry silicone or wax lubes but less than some of the heavier oilier lubes. It is also very easy to clean off the chain. I just replaced the chain on my 5200 at 3,500 miles and it had less than 1/16" stretch (which means I really didnt need to replace it). thats pretty damn good wear!!
Head set: Using the front brake and rocking the bike back and forth I can tell if it's loose. If loose, loosen stem bolts and press down while tightening stem bolts to take slack out of headset. Theres probably a better way to do this but this works for me.
dropouts: sometimes a creak develops in the wheel quick release mount where the steel quick release contacts the aluminum dropout on the bike frame. remove wheel, clean and re-install with proper quick release tension
seat post: clean and lightly grease the seat post where it contacts the seat tube and make sure it is properly torqued.
spokes: the stock Bontager wheels are very good. Unbelievably strong. no spoke noises on my bike
crank, BB, pedals, chainrings: The sealed BB shouldn't be causing noise but the threads in all these components should be greased and proper torque applied when installing them. Grease the pedal/crank arm threads, the crank spindle, the crank bolt threads and the chainring bolt threads. get a Park torque wrench and make sure everything is properly tight (see the excellent Park Tool website)
one irritating rattle I experienced turned out to be the shifter cable housings banging into each other on bumpy roads. the cable housings can contact where they cross each other in front of the handle bars. I tweaked them a little so that they had enough clearance to keep from hitting and that solved that noise.
now my bike is completely tight and QUIET... just the way I like it