There are total of 30 Diary Pages, 12 Alligator Eggs, 10 Mayan Statuettes and 10 Mushrooms
You can check your Progress under Start - Database - Stats - Exploration and / or Start - Inventory - Items.
I have a lot of spoilers used here to provide a better overview, simply fold the spoiler from your currently needed.
The clickable Timeline links will open in a new window and the video will start at the time or at the Item. In the Youtube Description you have the same Timeline too. Directly on Youtube dont open a new Window when you click a Timestamp. (Works only there)
I have created own Maps for each Collectibles. The Maps are cleared of any other Symbol (except Fast Travel). The Numbers on the Map match up with the Numbers in the Timeline except
the Diary Pages, here are on the Map the Diary Page Numbers for a easier find your missing Pages.Alligator EggsVideo:
Link: http://i.imgur.com/z5AjcqeMayan Statuettes
Two Mayan Statuettes can you find in DNA Sequence 4-6 and 6-1. You must complete this DNA Sequences to save the Mayan Statuettes.Video:
Before you can collect any Mushroom, you must complete the Sidemission in Bayou called "Bayou Fever" (Skull Symbol on your Map / "M" on my Map)Video:
Link: http://i.imgur.com/Qev8YCrDiary Pages
Diary Page 1 & 30 collect you automatically in the Story. There is no way to miss them.Video:
(Warning very large)