What's the significance of the grandfather clock in Elfen Lied?
My personal interperation of the clock was always that it symbolizes the start of a normal live for Kouta and company. Which in place would fit really well with the ending of the rhyme elfenlied which insinuates the 'elf' observing, hitting it's head on a stone with Cuckoo sounds.


  "What are those bright windows?
  There must be a wedding inside;
  The little people are sitting at the feast,
  And make merry in the hall.
  So I'll just take a peep inside!"
  — Fie! he hits his head on hard stone!
  Well, elf, had enough, have you?
  Cuckoo! Cuckoo!


Some people however, also suggest that it might be Nyu, as opposed to Lucy. With the clock chiming in the start or maybe even birth of Nyu, into the world of normal humans. 

Personally I think this was left open in a way it could be interpreted both in a positive and a negative ending. This both to drive people to read the manga which has a slightly different story and to stay in line with the rhyme, as this can be interpreted in both a negative and a positive tone.