Infernal Devices/WMG

Will went to Magnus about a cure for Jem.
If this troper remembers the end correctly, then Jem's had an attack not too long ago and his "illness" is beginning to look like it's going to be a significant plot point. Jem has mentioned that the Shadowhunters have been searching for a cure and never found one, but Will refuses to leave off, and it appears now that Jem's running out of time.
 * Jossed

Will is a Time Lord.
The cocky attitude and being a weirdness magnet make this guess seem pretty possible. His first encounter with Tessa also makes it obvious. I even this stele is another word for sonic screwdriver.

Will is crazy.
Just an idea that was planted in my head after reading Cassie's blog. It actually sounds pretty plausible, thinking back over the book's events.
 * This could go along with the guess above.

Jem is mad at Will in the teasers for Clockwork Prince...
... because they're lovers and Jem is jealous of Tessa! That, or Will is doing something incredibly stupid that could potentially ruin their relationship. Which, of course, is entirely possible.
 * Jossed. He was mad at will for wasting himself.

Will, not Jem, will die within the course of the series.
Just a throw at subverting the Incurable Cough of Death trope.

Magnus and Tessa are Half-siblings.
Both of their human mothers were tricked by a demon who could take on the appearance of their husbands!
 * Well they technically all descend from Lilith so...

Word of God said Magnus may have a new boyfriend in Clockwork Prince.
My bet's on one of the Lightwood brothers, or Ragnor Fell.
 * Or maybe Woolsey Scot, the respectable werewolf (confirmed as of clockwork prince)

Will is Alec Lightwood's ancestor.

 * Will and Alec both have blue eyes, but the Lightwoods typically are green-eyed.
 * This could possibly indicate that Will marries a Lightwood... possibly Gideon and Gabriel's yet unseen sister?
 * As of Clockwork Prince, Tatiana Lightwood is returning from her honeymoon.
 * Jossed, it's stated that Alec and Isabelle's Tall, Dark and Handsome looks come from Maryse, not Robert.