A lot of the clues, especially the ones we've come up with on our own (like my Aires Astronomy/Astrology links) are pretty silly. But there are still a few things that can't be ignored.
1. Iwata called finding information about the Revolution a "puzzle game" (I can't tell if he said formal puzzle game or form of puzzle game)
2. Reggie kept using the term "right brain", which is an esoteric term that doesn't fit at all with his normal straightforward speech patterns. The fake Nintendo On video showed something called a brain divided into hemispheres where the right side allowed you to create content... which of course fits with the old ideas about how human brains work, but why did Reggie start using it all of a sudden?
3. The Nintendogs demo had the wrong date AND the wrong time on it. One would've figured Nintendo, who pays such close attention to detail, would notice such a thing. The date showed was 5/19 at 10:10... the conference started about 10 minutes later than expected, so if it was on time we'd have seen it at exactly 10:00.
4. Right before the e3 conference, Nintendo.com had several very out of character videos featuring members of its staff on its site. One of the videos mentioned Thursday as an important day, then cut off like it revealed something it wasn't supposed to.
5. Nintendo.com had an unusual graphic on their site yesterday that said "Nintendo Now". The graphic didn't actually link to anywhere, but Nintendonow.com is the fansite that originally broke the Aries story.
Less damningly
6. IGN is the only major site that hosts the fake "on" video. They also just recently announced a partnership with Nintendo to develop the backend for their online content. They also showed a crude mock-up of the revolution based on the initial report of the size (3 DVD cases). But the mock-up actually may have gotten some other details right about the system... perhaps whoever made it had seen one before?
7. Aries himself. So far every prediction was accurate (including the backward compatibility all the way back to the NES). He said to expect a soft unveling at the Tuesday conference and something major on the 19th. Again we see 5/19 popping up.