In Eureka's "Once in a Lifetime", it seemed like a joke to have Zoey be valedictorian in a future that will never happen. But to be valedictorian, she had to smarter than a school full of geniuses; a subtle way to hint that Zoey is smarter than she gives herself credit for. We later learn this to be true when she scores a 157 on her IQ test, but tells her dad it was 112.
And how did Zoey end up with a super-genius level IQ with average parents? Well, that sort of thing can happen, but Jack mentions his IQ score was 111, which he was quite proud of because he didn't know it wasn't out of 100. However, he also mentions he "wasn't even trying". What sort of person can half-ass his way through a test and earn an average score without paying attention?
When the finale version of Zoe and Jack passed the one in the Pilot, they were in the sheriff's jeep instead of Carter's car, with Zoe not waving at herself as the other one did in the pilot, but with the timeline change, this could have been the way it happened in the changed timeline all along.
If Henry and Grace were working with Beverly, that would explain why Beverly turned to them to help out with the Matrix incident. Henry didn't know it, but at some point in the past, they'd worked together already.
You know how Henry's hatred of Jack for stopping him from using time travel to save Kim was apparently forgotten by the writers? In the episode "God is in the Details," Jack and Henry work together to stop the church pianist from using a dangerous device that she thinks will let her see her husband in the afterlife. Afterwards, Henry consoles the pianist, reminding her that their loved ones are in Heaven and they will be reunited with them soon. This is the point where Henry forgives Jack.
Taking the Historical In-Joke to its logical conclusion, if the Einstein-Grant bridge became the Einstein-Rosen bridge after the timeline changed, then that means EVERYTHING prior to the Season 4 premiere occurs in an alternate universe to our own, and it is only now that history is put "right". It may never be significant, but it is an odd thought.
Considering in the new timeline, Kevin no longer has Autism and thus no longer possesses the unique connection to the Artifact that drove everything in the first two series, you have to wonder... what exactly happened to the Artifact in the new timeline?! Does it still even exist?!