These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The stick figures: sentient beings tortured and enslaved, or simply some self-inflicted malicious code? note This one has an In-Universe application, as an anti-virus program in 2 recognizes the Chosen One as a virus.
HSQ: The Chosen One and the Dark Lord wrecking the Animator's computer at the end of Animator Vs Animation 3.
Jerkass Woobie: 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.
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.
Stop Helping Me!: Subverted. You'd think Clippy offering his help to the Animator would be quite ineffectual like in real life, but he turns out to be a surprisingly competent fighter.