The stick figures: sentient beings tortured and enslaved, or simply some self-inflicted malicious code? note This one has an In-Universe application; On one hand, Avast! Antivirus recognized the Chosen One as a virus in 2. On the other hand, several side-ad links in the beginning of 3 imply that stick figure enslavement isn't an uncommon occurrence.
Also in episode 3, when the two sticks teamed up, was it because The Chosen One showed who the Dark Lord's real enemy is or did he force him to work for him under the threat of death?
Yes, the Animator's technically the Big Bad, but given what a dangerous psycho the Chosen One is, it's hard not to feel bad for him and the icons who come to his aid. As a matter of fact, some viewers thought the Animator was the good guy.
The Second Coming starts his revenge by going out of his way to insult all of the Animator's FB friends before escaping to his phone and destroying its UI, but considering this was prompted by the Animator basically murdering all of the Second Coming's friends right before his eyes, its hard to blame him.
Rescued from the Scrappy Heap: In 3, Clippy. The usually irritating animated paperclip assistant from Microsoft Word manages to give The Chosen One a good fight.
Visual Effects of Awesome: The animation gets better in each installment, but special mention goes to "Vs. Minecraft"—According to the BTS, adding the diamond armor to every character required hiring additional help (it would have taken an additional month or two otherwise), and in the scene when the Creeper blows up and launches around 100 arrows that were stuck to the dirt blocks surrounding it, he took the time to animate the trajectory and landing of each individual arrow rather than taking the easy way out and copy-and-pasting the animation paths.