The handyman knows more than you think.
In Tourist Trapped, Soos says "My wisdom is both a blessing, and a curse." What does he mean by that? And what happened to his wisdom in later episodes?
In The Time Traveler's Pig, we see Soos (in the beginning of the episode) saying exactly what would happen later in the episode. Can he see into the future?
In Fight Fighters, Soos shows his smart side again with his use of the word "amiable", as well as his quick thinking.
In Summerween, Soos shows his secret smarts again. When he and the kids are hiding from the Trickster in the store, he wishes out loud for some kind of disguise. Secretly, he knew full well that he was in a store which sold costumes. Similarly, a few seconds later he was playing with the cackling skulls. This was actually his attempt to get eaten, eat his way out, and save Gorney and the kids, all without looking like a genius.
More proof comes from Bottomless Pit - Soos' Really Great Pinball Story. He apparently knows every inch of the pinball machine. He's obviously been zapped into it before, giving more evidence that he knows about the Gravity Falls weirdness.
In The Deep End, Soos thinks the inflatable pool ducks are alive, and that their revolution is at hand. Although Soos does look stupid because of this, he may be onto something. I for one was wondering why the Gravity Falls pool has inflatable ducks if nobody is allowed to touch them. This may be yet another hint that Soos knows more than you think he does.
In Carpet Diem, we see traces of Soos' smart side again. He tells Dipper and Mabel that the room "gives [him] major creep-o vibes." I'm pretty sure he knows who used to occupy the room. Maybe Stanford told Soos about his brother shortly after hiring him, and Soos figured out that the room used to belong to Stanley. (According to my timeline, Soos would have been hired less than a year after Stanley's disappearance.)
In Dreamscaperers, Soos finds the door to Stan's lab in Stan's memory, and then quickly closes it. It's obvious he wants to protect the twins from finding out about it.
Later in the episode, Soos (in Stan's memory) looks on as Stan (also in his memory) explains the power of the mind to Dipper.
Bill Cipher outright admits that Soos is more clever than he looks later in the same episode (although Soos tries, probably unsuccessfully, to hide it).
In Gideon Rises, when Mabel asks what Stan would want with the journal, Soos conveniently distracts Dipper and Mabel. Many believe he planned this to distract them from the truth.
We see more of Soos concealing his smart side in DGTTU - Candy Monster. Soos calls the Candy Monster "Grunkle Stan". Obviously, nobody is that dumb (except Deputy Durland or Nathaniel Northwest); instead, Soos is trying to act dumb to save his image.
Soos shows his smarts more openly in Fixin' It With Soos. He manages to fix up items relatively quick, as well as sprucing them up and making them amazing.
Soos finds the laptop in Into the Bunker, and while it may have looked like an accident, I believe it was on purpose. He knew about the laptop and picked it up without looking smart. He then fixed it up within a few days, but Dipper couldn't get in because he didn't know the password. I think Soos added the password to keep Dipper out for some reason. This is further proven in Soos and the Real Girl when we see a Post-it note with the password FIXINIT1. That has 8 characters, which is the same number as the laptop's password.
Society of the Blind Eye shows something very odd. When Soos is listening and singing along to Straight Blanchin', he says that if rappers told him to eat his own pants he would do it. The song then told him to eat his own pants. Notice that Soos has obviously heard the song before, so this is more than convenient timing.
One day...wearing the fez
Soos tries on Stan's fez and says "One day..." This could have two meanings. The first and more common explanation is that Soos hopes to one day own the Mystery Shack. In Boss Mabel, wearing the fez seems to symbolize running the Shack, so this could be true. The second theory is that Soos is part of the ROotHM, and wants to obtain Stan's high position, which is symbolized by the fez.
Does he work for free?
Stan mentions in Double Dipper that Soos works for free. But in Carpet Diem, he attempts to give Waddles (in Soos' body) a pay cut. According to the transcript on the wiki, the line is "because you'll work for free..."
In The Legend of the Gobblewonker and Fight Fighters, it's revealed that he owns a boat and pickup truck respectively. How is this possible if he doesn't have a source of income?
In Gideon Rises, we find out that Soos' grandmother is poor. If Soos lives with her and makes money, shouldn't he be taking home a portion of it to help out?
In DGTTU - Stan's Tattoo, Stan says he will pay Soos to put his shirt back on.
Christ figure
A theory out there is that Soos is a Christ figure. Makes sense. His name is short for Jésus, which is Spanish for Jesus. He seems to (sometimes, anyway) be the smartest and greatest human being ever to live.
