I know what you mean. I think it comes from within. If you are beautiful and lovable inside, it kind of shines through in your face and posture. The opposite is also true. I know people who are physically attractive, but so malicious, petty, greedy and vulgar that it ruins their looks.
In my experience, they:
Have a good sense of humour and can laugh at themselves. Not taking yourself seriously is a lovely trait
Never talk about others behind their back
Are cheerful
Are kind (not in order to look good, or poke into other people's lives, but because they hate to see their neighbours suffer)
Are real – not false or fake
Never show off, or try to out do and belittle others.
Take no pleasure in other people's misfortune (while pretending to care)
Are their own person. They don't follow the crowd, and don't creep around the dominant alpha types. If they believe something is wrong, they will go against the popular and cool people. Being your own person, having a strong moral code, and having the confidence to do your own thing is so attractive. Some people are so herd-like. They have to be reading and watching what everyone else is reading and watching.
Have a genuine and deep sympathy for other people (not that sickly, fake "I'm here for ya babes" nonsense)
Have goodwill towards others – I mean, they don't begrudge them happiness or success
Are interested in other people without being nosy. There is a big difference. Nosy people fish for gossip and misery. They want to know how much you earn. And they want to hear about your failing marriage, or your daughter's crap GCSE results, etc. Being interested in people is different – it means wanting to know their favourite novel, their favourite paintings, their spiritual beliefs, etc. Above all, it means listening.
Have class. I don't mean money or a private school education or a silly accent. I mean they know how to behave – eye contact, smiling, not talking over you, not screeching with fake laughter, not boasting...pleasant manners, etc.