Spoilers and all.
Let the Right One In plays on the vampire tradition that the vampire must be invited into a home, and the motif of meetings at doorways and windows repeats throughout the film. However, I believe that letting the right one in refers to an internal conflict--to badly oversimplify, to "let the right one in" is to resist the evil within oneself.
Let's take a brief gloss at some key images and moments throughout the movie that might support this understanding.
--one of the first images we see is the distorted reflection of Oskar as he looks out the window. He is in the process of practicing to murder some school bullies (he is also doing such practice the first time Eli appears to him, further supporting this interpretation). Given that he collects news stories about murderers, it is fair to believe we are watching a killer develop.
--Eli tells Oskar that he must fight back against the bullies.
--Oskar does fight back, hitting the lead bully in the ear with a stick. After doing so, his face has a look of ecstatic pleasure.
--When Oskar first comes into Eli's apartment (and learns for certain she is a vampire), he is touching her hand through the glass on her door. She keeps moving her hand around, and he keeps following to try keep covering it).
--Eli tells Oskar that she is like him: he has murderous desires. She tells him that he must repress these--she kills because she has too (her consumption of blood is usually portrayed as an animalistic compulsion). She tells Oskar to "be like me a little."
--Eli offers Oskar some money--he disgustedly rejects it, knowing it comes from her victims.
--After Oskar saves Eli (not entirely intentionally helping her to kill her potential killer), Eli thanks him and leaves, and again we see the the image of Oskar's reflection through the window as he touches the glass. At this point it is difficult not to see the parallel--Oskar touching the hand of his reflection in the glass, Oskar touching Eli's hand through the glass. She is, in some ways, a reflection of himself.
--What follows is the most frightening scene in the film: an even more dangerous bully joins the earlier gang of bullies, and Oskar is seriously threatened. He is not in a position to fight back, and he passively acquiesces to the violent threat. He is saved by Eli, and their eyes meet and they smile at one another.
--The final scene (Oskar on a train, signaling Morse code through a box that may contain Eli) suggests Oskar is Eli's new mortal servant.
After developing this interpretation, I'm still left with a lingering question: did Oskar "let the right one in"?
He did not violently defend himself--yet he was in no position to do so. But Eli's rescue was extremely violent, and if he now works as her mortal servant, we know he will likely be asked to perform rather nefarious deeds (we've already seen Eli's previous mortal servant committing murders and disposing of bodies). But maybe letting in the violent side is, within the film, the "right one." Or maybe letting the right one in refers to Eli's choice of Oskar.
I'm posting this fresh, without tainting my ideas with the ideas of others; I'll now check out some reviews and see what other angles have been taken.
Reading Manohla Dargis' NY Times review, I recall that Eli kisses Oskar while there is still blood on her lips. Dargis points out that "Eli seizes on Oskar immediately, slipping her hand under his, writing him notes, becoming his protector, baring her fangs."
Other reviews: Roger Ebert, Carina Chocano , Angela Kaelin, Ben Kenber (who writes, "Of course, there will be more moralizing over what Eli has done and how Oskar should (in the eyes of many) respond to it." Perhaps that's what I'm doing, though interpreting the movie as an internal conflict isn't exactly "moralizing," and at any rate Eli seems to offer moral advice to Oskar), Jonathan Kiefer, Roger Moore