There are 55 total side quests none of which are missable. You can backtrack to earlier zones at most points in the story and after the final story quest is done. The final side quest does not become available until after the story is complete.
There are four types of quests.
25 general ones
10 Historian quests
10 Hunting quests
10 Wanted quests
The Historian, Hunting and Wanted have achievements for finishing the set and each set rewards a Legendary piece of gear. You must return to the quest givers to hand these in and get the reward. The reward is tried to your level and World Tier at the time you finished the objective so there is no point in stock piling the quests for better rewards.
One of the general ones, Outsiders Legacy is a large multi-stage quest with its own achievement tied to it too.
For the most part they're very straight forward but at time of writing the waypoint tracking can break in later missions leaving you to try find the location. Usually this can be fixed by traveling to another zone on the world map and then back again. It's also on the list of known issues so it will hopefully be fixed in a later update.
One that may give you trouble is a hidden quest called Forgotten Chapel in the Canyon of the Grand Obelisk, a video guide on how to unlock it has been included below. (Thanks Kenshira and Raptor Demon)
The final quest will be available in the camp/garage area in Rift Town after finishing the main quest. If it's not there talk to Channa about Jakub and it should force it to show up.
If you want to check your progress you can do so by going to the Progression section of the Accolades and looking at the Philanthropist accolade. The world map also has a break down of what you have completed.