For my 13 year old son--
Homestuck: Book Three, by Andrew Hussie. Books one and two are out of print and too expensive at this time, so I hope he doesn't mind having just this one. Since he loves Homestuck, it should be ok.
Year of Yesh: A Mutts Treasury by Patrick McDonnell. Because all 13 year old boys need love and cute.
Buffering: Unshared Tales of a Life Fully Loaded by Hanna Hart. My son took John Green's recommendation to heart, and this is the only book he specifically asked for. I'm not quite sure what he'll make of it; the blurb references lesbian sex, which might make him blush (the sex part, not the lesbian part).
Rocks Fall Everyone Dies by Linday Ribar. I pointed this one out to him in the bookstore, and the cover and title appealed mightily.
The Answer (Steven Universe) by Rebecca Sugar. This turned out to be a bit on the young side, but he's a fan, so he'll enjoy it at least for one read.
For my 16-year-old son--
Mostly Void, Partially Stars: Welcome to Night Vale Episodes, Volume 1 By Joseph Fink. Night Vale of course is geek teen staple, and I'm hoping his fan enthusiasm carries over into reading.
Hilda and the Black Hound (Hildafolk) by Luke Pearson. He just read the fifth Hildafolk book for his work as a graphic novelist for the Cybils Awards, and happened to mention that he'd never read this one, and that really he'd like to own the whole series (which isn't going to happen this Christmas...there are limits).
Lowriders to the Center of the Earth (Book 2) (Lowriders in Space) by Cathy Camper. He wanted it for his graphic novel collection.
The Arrival, by Shaun Tan. Another asked for because it was a gap in his collection.
(Here's his graphic novel review tumbler, if anyone wants the authentic target audience opinion....)