TV Guide did an interview with some fan questions. Some interesting insight...

What's up with those symbols (leaf, frog, etc.) that appear before commercial breaks? Are they some kind of puzzle that we're supposed to "figure out"?
Well, not exactly. "They are all things that look natural, but have more to them; they've been altered," says Orci. For now, he advises only that you note the order in which they appear on the series. For the record, so far we've only seen the leaf, which was floating around inside the Massive Dynamic handprint scanner in the final scene.

Why was Walter Bishop institutionalized in the first place? Sure, he's eccentric, but most of the time he seems perfectly lucid.
"He's certainly not cured of his ailments," Orci warns. "There will always be two steps forward, one step back [with Walter]." He said that viewers should be asking themselves: Was Walter's therapy in his best interest? How will being away from that therapy affect him? "If he seems lucid, it's just a fake comfort zone to put the audience in," he says.

Why do they have a cow in the lab? I know they said something about similar DNA, but why not a monkey or rats like they usually have in a lab?
"The question is, who is the cow really working for?" Orci jokes. He echoes what Peter Bishop says in the script: A cow is an ethical test subject, and its blood was used to synthesize the concoctions that saved Agent Scott's life. It probably doesn't hurt that walking a cow through the hallowed halls of Harvard makes for better TV than, say, a cage of rats.