It could be skin oils, dead skin, a build up of lotion or acne medication, particles of food (if you're one of the folks who likes to moisten their lip plate with saliva before playing), etc. If you want to try cleaning it off, get a bit of denatured alcohol and a soft cloth/Q-tip and see if you can't remove some of the residue.

Yes, I agree with Chris. I wipe mine down every now and then with rubbing alcohole and this helps. I am unsure about the pretty scratches though that you mentioned. I don't have any scratches on mine and never have so I am not sure how that happens?

what type of flute do you have?
if its dull the plating could be wearing off.
but that only really happens to lower end flutes.

what type of flute do you have? if its dull the plating could be wearing off. but that only really happens to lower end flutes.

That's not really true. I have a Yamaha flute that's the equivalent of the current 684HHV that's about 16 years old, which would cost you about 3K new (certainly not a lower end flute). It has a plated mechanism, and the plating on the G# key is wearing through. It's not the overall quality of the flute that will dictate when or if plating is going to wear through, rather it's the quality of the plating and the care that's taken during the preparation and the process itself. Poor plating is not necessarily indicative of low quality instrument, nor is good plating necessarily the sign of an excellent flute.