What is Kaworu implying at the end of RoE: 1.01? I've rewatched Rebuild of Evangelion: 1.01: You can (not) advance, and something struck me.
At the very end (so spoiler):


  Kaworu is on the moon, looking at Shinji, and say "You're the third again, Shinji"


Is the "again" a sign that what happened in NGE/EoE in the same continuity? Or does it link with RoE 3/4 (which I've still to see)?
It's up to interpretation and there hasn't been, as of yet, any sort of official take on what a lot of the cryptic stuff that Kaworu says. If you'll recall, he also calls Gendo "Father". The line you're referring to is probably more something like:


   "The third again? You never change. I look forward to meeting you Shinji Ikari."


Not that Shinji is the "3rd" again so much as referring to Shinji as "3rd" and saying he's up to something "again".

Lots of ways to interpret this in light of some of the other things:


Kaworu and Shinji may have met a long time ago, and when Kaworu mentions looking forward to meeting him again, it's in reference to a previous meeting which Shinji may not have either been aware of or remember
Similar to #1, it may have been that Kaworu was a silent observer through a lot of the previous chronology before the start of the first film, enough so to have felt that he has personal ties with the family, thus also referring to Gendo as "father"
Going along the veins of #2, there's also an off-hand mention of a "Pact" with Lilith in the 3rd movie, this could all have tied into how Angels in general play a different role in this continuity than in the original TV series. It's possible that Angels have been interacting with humans well before Sachiel's attack in the first film and that Kaworu may be referring to that interaction.
Venturing in to even more speculation, there is the "Sequel" stuff. Some people interpret Kaworu's language and how he's acts as he's met Shinji before
as evidence that Kaworu is either some sort of time traveller, that the new films are a thematic or chronologic sequel of the original TV series (and for some reason, Kaworu alone remembers the events from the TV series), or there was a world "reset" after instrumentality of the TV series (and again, Kaworu is the only one that remembers those events). Can get even wilder with speculation, but you get the idea.