It seems to happen whenever the PS3 is loading a game or something. Like when Uncharted  2 starts up when that dagger is spinning the disc drive makes some noise. then it goes away once it is done loading. Is this normal?

I can't speak to whether or not it is a "bad" thing, but it happens with my PS3 as well. I have a Slim 120gb (with a 320GB HDD, not that that probably matters). Like you said, it happens during loading times or startups and it sounds almost like the disk is skipping. I'd like someone to comment on this.

(IMO) the sound seems normal to me. In comparison to my 360's Elites disk drive, the PS3 is very quiet, and they both work perfectly.

Mines make noise when it's face down. When I stand it up sideways it's quiet.

Mine is standing and it's making the noise, don't know if it does facedown though, It's not a good position for where I have it.