A NAVAL NOD
If you've been working your way through the Naval Missions you will have spent plenty of time on your ship, the Aquila. The name Aquila is particularly significant here as it's the Latin and Romance language word meaning 'eagle' - a symbol often used by the Assassins, appearing at Viewpoints and of course as a basis of your Eagle Vision ability.
Carrying the significance even further, there's also a star constellation named Aquila whose brightest star just happens to be... Altair - the name of the original Assassin's Creed protagonist, which is an abbreviation of an Arabic phrase meaning 'the flying eagle'.
YOU'VE GOT MAIL
During the course of the main story you'll see a number of pop-up notifications appear, alerting you to the arrival new email messages. Unlike the other notifications of information being added to your Animus Database, these emails can only be accessed by exiting the Animus.
After you reach the end of Sequence 3 and return to the present day, you can interact with the free terminal next to the Animus then choose the email option to catch up on your correspondence. Keep checking on this during the course of your playthrough for messages from your colleagues and even posts from Juno herself!
You can also use the terminal to replay Desmond's missions should you be so inclined, but be aware that once you finish Sequence 12 you will be locked into the Animus so after that point this area of the game is no longer accessible.
THE BULLETPROOF KIDD
Collecting the Peg Leg trinkets scattered around the maps will open up additional Naval Missions, after you return them to Peg Leg on the Homestead docks. Completing four of these Captain Kidd's Treasure Missions unlocks the final trial on Oak Island.
Once on the island use Eagle Vision to find the four clue points, then solve each puzzle they reveal by rotating and positioning the highlighted overlay so it lines up with the glowing objects in front of you. This will direct you to the entrance of an underground area, which you need to climb through and investigate.
Inside you will discover a ring with mystical magnetic properties, which turns out to be a Shard of Eden. When you arrive back at the docks you'll hear a voiceover from Shaun, explaining that the Shard is a First Civilization artifact which will greatly reduce the chances of you being hit by bullets when facing armed enemies. This proves particularly useful for beating the optional objectives when replaying certain missions where you need to limit the amount of damage you take from opponents.