In looking at some of the unanswered questions from Season Two, I believe a few may have been answered. Along with those, I thought I'd share some theories on other unanswered questions.
On the few I believe have been answered, figured it was better to do this in a blog post rather than on the episode talk pages (since it contains some speculation and I wanted to get the feel of how many people agree with me about what questions may have been answered).
Happy New Year: Who hired Lobo? -- I believe this question was answered in Alienated, in which the Kroloteans discussed how their work had been exposed. One of them said it was the work of the Competitor (the Reach) and asked "Who else hired the Main Man to expose us?" And Lobo has been identified as the Main Man.
Beneath: How did Psimon know about Batman being out of the picture? -- I would assume it is because Vandal Savage has been making his way to Rimbor and knows about Batman and the others standing trial. That one, though, may be up to debate as to whether or not Savage was on Rimbor at that time.
Bloodlines: "Crash the mode" meaning -- Is there enough information to suggest that it means that something happened that kept events from taking place as planned?
Depths: Why did Black Manta want to destroy the Earth-Mars communication satellite? -- This hasn't been confirmed on an episode but I suspect it will be revealed that the Reach took over Mars.
Darkest: Why was Shimmer in a pod next to Lagoon Boy? -- Do we believe enough evidence exists that Shimmer was being used as one of the Reach's test subjects? Events in Before the Dawn seem to suggest this.
Before the Dawn: What powers did Shimmer acquire? -- Should the events in Intervention make it clear that the question has been answered?
The Hunt: Crystal key questions -- Seems to me with the Reach and the Light, it's about trying to gain control of the Warworld. Again, not confirmed in an episode but that seems the likely answer.
Note: Going through the unanswered questions, I did find one that has been answered and made the appropriate change.