According to Steve Holland who is the show-runner starting with this season, Wil Wheaton will return in this season since his absence from Season 10. And this has confirmed to be true since it has been stated that he reappeared in "The Proton Regeneration" (S11E6), along with Professor Proton, their first appearances since "The Opening Night Excitation" (S9E11) and "The Celebration Experimentation", respectively and a span of 43 episodes and a span of 37 episodes, respectively. Wil also returned in the 15th episode. Wil will also return for Sheldon and Amy's Wedding.
I read through the article and all the comments (which makes me miss TBBT even more and it hasn’t been off the air a week yet) and noticed that 3 of my favs aren’t mentioned. (1) episode where a bully (Todd Sornecki) steals Sheldon’s online trophies and Penny kicks him in the nuts for Sheldon; (2) the episode where they reveals each others secrets (Leonard slept with Priya; Raj used Sheldon’s tooth brush; Howard told Raj foreigner give gifts to Americans for certain holidays and Sheldon put moths in Leonards food “for science”; (3) the episode where Amy and Sheldon go to the aquarium “as friends”, when Sheldon tells Amy “I can handle a lot of things Amy but getting over you isn’t one of them, I think we should just be friends” it breaks my heart everytime; (4) the episode where Priya buys Leonard glass and he walks into the cafeteria and causes mass chaos, that’s a classic; (5) the episode where Priya ruins the roommate agreement between Sheldon and Leonard, when Leonard buys Sheldon Greek food it’s hilarious. Sheldon gets back at Leonard & Priya by threatening to send an email to Priya’s parents telling that “she’s in a relationship with the whiter than marsmellow fluff Leonard Hofstedter”. Ok just one more, when they all take a road trip to speak at the science convention and Bernadette runs into her former professor/lover played by Rick Foxx and Sheldon banished Penny to the “love car” and Bernie and Howard sing Sonny & Cher “I got you Babe” is funnier than hell. I still crack up when I see Raj look down at Howard’s junk to measure Howard’s junk against Rick Foxx’s, I can’t believe the sensors let that through.
After learning Sheldon went behind their backs to work with the military again, Leonard and Howard say Sheldon is like Thomas Edison, taking credit for others' ideas, while they are more like Nikola Tesla. Leonard and Howard bring in Barry Kripke to help create a better idea than Sheldon's, but Kripke goes to the military himself, cutting all three of them out. Meanwhile, Bernadette fears Ruchi is trying to steal her projects at work while she is on maternity leave and enlists Raj to spy on her. Though he finds proof that Ruchi may be stealing from Bernadette, Raj tries to defend Ruchi like a boyfriend would, pointing out Bernadette's hypocrisy as she would most likely have stolen from other people's projects as well. Ruchi is not happy about this and promptly dumps Raj.
Sheldon and Amy are surprised to find that Wil Wheaton's new Professor Proton show is actually very entertaining and that Wil had Howard on as a guest. On Howard's suggestion, Sheldon apologizes to Wil, mending their friendship, and tells him he wants to be on the show; but Wil asks for Amy. Sheldon tells her to do it, but she says she often doesn't do things to avoid upsetting him. Sheldon is horrified when he realises how selfish he has been, especially when he finds out that the men do the same for him. Sheldon encourages Amy to go on the show to inspire girls to pursue science while trying to control his obvious jealousy for her. Meanwhile, Leonard writes a book about a physicist that solves a murder, the protagonist Logan Dean is based on himself. Bernadette points out Logan's mean boss Illsa is similar to Penny, who thinks it is based on Bernadette, though Leonard does not correct her. However, Bernadette tells Penny the truth, upsetting her and making her mad at Leonard. After calling his mother for advice, Leonard learns that Illsa is actually like her; but abandons the book when he realizes he wrote romantic tension into the relationship between the characters.