Perhaps we’ll have some answers, at least, before the end. I always dreamed of dying well-informed.

Sand dan Glokta, Last Argument of Kings

Unanswered Questions remain from the trilogy and the stand-alone books. "Solved" denotes those mysteries that the books completely solved. "Unsolved" denotes those that the books barely addressed. "Partially solved" covers the rest.
Partially Solved
Topic Question
What is the cause of Logen Ninefingers berserker state, the Bloody-Nine? There many theories of Demon possession, Spirit possession, berserker rage, and simply split personality. Or could it even be an actual God, since he sometimes refers to himself as the Great Leveller.
For that matter, why can Logen talk to Spirits? Is it related to Bedesh? Is it somehow related to the Bloody-Nine? Two special abilities that are unrelated seems unlikely.
Why exactly did bad blood develop between Logen and Bethod? It's hinted at but not fully explained.
What happened to Bedesh? He's not heard of again after taking the Seed to the Edge of the World. He seems to have died somehow before the death of Kanedias.
What has Ferro been doing since the end of the trilogy? She’s last seen heading to Gurkhul, possessing some pretty awesome powers from exposure from The Seed. There's only one tiny hint in Best Served Cold, when Ishri comments, "My brother was killed. By a woman seeking vengeance."
Are Bayaz and Khalul as bad as each other? Bayaz likely betrayed and murdered his own master Juvens, and later his lover Tolomei, to hide this secret. Bayaz is driven entirely by ego and spite, wanting nothing more than to crush Khalul for daring to oppose him. Khalul claims to have only fallen to darkness in order to bring Bayaz to justice, but does that really justify slavery and forcing victims to become Eater?
Is Bayaz an Eater himself? He is seen eating some quite raw meat in his encounter with Calder near the end of The Heroes. At least two of his apprentices are Eaters, and Bayaz has no qualms about breaking Euz's First Law to gain more power, so breaking the Second Law may not be out of the question.
Who killed Juvens and why? It’s certainly heavily implied it was Bayaz, but why? There are only some vague comments that Juvens was an idealist, and wanted to make the world a better place through good intentions, which Bayaz believed had no chance of working. Differing values seems a weak reason to kill someone, especially since Juvens forgives Bayaz for betraying him, and taking Kanedias as his new master.
How did Tolomei die exactly? It’s certainly heavily implied it was Bayaz: Yulwei’s recalls that Kanedias fell first and then his daughter, and Tolomei herself indicates that Bayaz threw her off the bridge, but why? There's only a vague comment that "So that you <Bayaz> could keep your secrets? So that you could seem noble?”. One good theory, which is probably the truth, is that Tolomei knew that Bayaz himself secretly killed Juvens. Kanedias knew who killed Juvens, and would surely have told his daughter.
Where in the world are the Magi Leru and Karnault? For that matter, there are three Magi who have yet to be even named. What happened to them?
Is Khalul's temple-fortress in Sarkant the Great Southern Library? For that matter, where is the Great Eastern Library?
Where is The Seed now? It was last seen, being carried away by Yoru Sulfur and Bayaz when he left Adua at the end of the trilogy, but where exactly is it? It's presumably in the Great Northern Library. Given it's immense power it's hard not to assume it may play a further role.
What caused Shenkt and Bayaz to fall out? It’s certainly heavily implied, that Shenkt got tired of kneeling before Bayaz' chronic megalomania.
Is Shenkt the celebrated King Casamir of The Union? Vitari's pet name for him is Cas. It is quite striking that Bayaz seems to have a particularly low opinion of King Casmir, referring to him as a coward. It seems plausible that Casamir/Shenkt was not only Bayaz' pawn as King, but also his apprentice and an Eater.
How did Caurib learn to do real magic? She certainly possesses real power, but how did she learn. When she uses magic, does she touch The Other Side like a Magus?
Can anyone train to be a Magus or do you need some kind of innate ability? For that matter, it is said that you need some kind of “promise” or innate ability to become an Eater. What are the innate abilities? Are they the same one?