My theory: just do it. Allude when it feels right, and for pete's sake, don't footnote the things. It's too self-conscious. Just let the writing and the story be themselves. As the first creative writing teacher I had used to say: Never apologize. Never explain.
This Cassandra Claire crap, though, is plagiarism, not allusion. Entire sentences lifted: bah. It's gone beyond allowing one's phrasing to be influenced and moved right into thievery. Footnoting it wouldn't help.
And yet: Philip Pullman retelling "Paradise Lost", a-okay. Shakespeare borrowing all his most famous plots: a-okay. Because everything else: not borrowed.
There's something about CC's "borrowing" that is exactly at the level of writing that really ought to be original. Right at the places I'd think of as the best places to strut my personal style and craft, this fanfic writer chooses to insert two entire sentences from Gene Wolfe. Okay, great taste there on the ripoff, but... the impulse makes me suspicious. Sayers puts her quotations into the mouths of highly-educated characters witticizing at each other; she doesn't use them to describe Lord Peter's experience in the belfry while the bells are being rung.