…. i say thankyou! 
– i’m thanking them for being kind and thoughtful enough to try and say something nice to me, for taking the time to do something that they think will make me happy.
…..whether or not i think they’re existing in some kind of alternate reality where my haircut is cute/handwriting is nice/i’m kind and funny, or they realise that i feel like dying inside over the fact that it has become apparent that i was pretty noticeable instead of managing to be the stealth ninja-chick i was aiming for, they did make the effort to say something nice, and it just shoots them down if i brush it off.
refusing to accept a compliment is kinda like ….someone trying to give you a present that they’ve chosen just for you, and unwrapping it infront of them, and handing it back because you don’t want it….. a bit rude. although quite often i think ‘yeeeeaaaaah, they must be a bit mental to think i’m funny/clever/whatever’ later on, at least they bothered to try and give me a nice guesture, so i aint gonna shove their gift back in their face (i just mentally donate it to charity in private).
giving one back can help to minimise discomfort as well. it doesn’t hurt to say ‘awww, thankyou- thats really kind/sweet/thoughtful of you to say!’ with a big grin. then they walk away feeling good about themselves, even if you can’t manage that yourself (and doing something nice- like thanking them- gives you something to feel good about!).
it’s taken me a long time to get to the point where i can accept a compliment at face value without being suspicious or dubious and thinking “ok, what do they want?’ but i’m getting there. and at least i don’t SAY “ok, what are you after!?” and give them a shifty look any more….. thats a start!