Here's a list of some of the unresolved plots from over the years...Add your own if you remember any!
1) Marlena's missing years -- We know she spent 9 months pregnant with the Gemini Twins, but she was on Stefano's island for 4 years. We know her taught her chess during that time. But what else happened? Was it similar to how he used Hope when she was presumed dead?
2) The Marlena "Clones" -- Around the time of the possession storyline, Stefano sent about 5 Marlena lookalikes (played by Deidre Hall) around the world to fool the authorities as he planned to kidnap Marlena. Who were they? Where are they now? Are they really clones? Could they be connected to Marlena's missing years?
3) Hattie -- What was the deal with Hattie? Stefano never ended up going through with his plan to switch Marlena with Hattie. Why did she resemble Marlena? Could they have been cousins? Could Hattie have been an amnesia-stricken, not-dead-after-all Samantha Evans?
4) Stefano's freezer/Jonesy's townhouse
When Jonesy was taking care of Stefano's townhouse, there was something secret in the freezer in the basement. We never found out what it was!
5) The jungle compound
When John and Hope visited Stefano's jungle compound, there was something secret being kept under a tarp by Dr. Rolf. What was it?
6) Wendy's son Ben
Remember Wendy and Jonah? She had a son Ben and we never found out who his father was even though he began stalking them just before they last appeared on the show.
7) Greta's father
Before dying, Princess Gina told Greta that her father was someone in Salem. We never found out who it was, but before leaving town, Greta revealed that he was not John Black. So who was he? Stefano? Victor? Roman?
Jonesy's Freezer: In my opinion, the freezer contained Andre DiMera's cryogenically-frozen body. Just follow me on this one! When Andre (posing as Tony) faked his death in Aremid, he was dying of a fatal blood disease. In setting up his fake death, Andre decided to freeze his body until such time a cure could be found. When Stefano, who had amnesia at the time of "Tony's" supposed death, recovered his memories, he learned that Andre had stashed his frozen body in one of Stefano's safehouses in Salem. When Vivian came close to discovering it, Stefano had the body shipped to a Caribbean island. The freezer was set to defrost after 6 years, and Andre awoke in 2002. Learning of Stefano's near-fatal car crash in Monte Carlo, Andre scooped up Stefano and regularly drained him of blood, transfusing it with his to cure the disease.
The Jungle Compound: The item at the jungle compound was either one of two things: Firstly, it may have been one of the forged paintings "Gina" created for Stefano. Secondly, and more likely, it was the x-ray machine Dr. Rolf brought to Salem that allowed Stefano to view the masterpiece underneath the forgery.