From here:
http://www.iaaf.org/athletes/biographies/country=JAM/athcode=184599/index.html
2001 - 21.73 (age 14)
2002 - 20.58 (age 15)
2003 - 20.13/45.35 (age 16)
2004 - 19.93 (age 17)
2005 - 19.99 (age 18)
2006 - 19.88/47.53 (age 19)
2007 - 19.75/45.28 (age 20)
Looking at this, a few things jump out at me.
First, most obviously, is how fast he was at a young age. 20.13 and 45.35 as a 16 year old. Damn. Now that is some natural talent.
Second, this looks like a clean progression. No huge drops in times after the age of 15. Just tenths of a second, every year. Little by little. Took him 5 years to go from 20.13 to 19.75 - yeah, that sounds about right.
Third, the fact that he ran 19.75 last year showed that he was ready for some amazing things. Remember that before Michael Johnson, the world record was still 19.72. Bolt was knocking on that door last year.
Fourth, the fact that Bolt can run 19.75 but "only" 45.28 leads me to believe he's more of a speed guy. There are 800 runners who can run 45.28. If Bolt is only running that, he must be running on fumes by then. To me, this suggest he should be outstanding in the 100.
It seems likely to me that he's clean. It's a sad state of affairs that my first instinct would be to doubt him, but I look at this and I think he is clean.