Well if you are looking for the chronological order of the books/comics in regards to the in-universe timeline - that order is as follows:
"The Forerunner Saga" (millions of years in the past)
‘Cryptum’
‘Primordium’
‘Silentium’
Prior to and in between ‘Halo’ games 1-3
‘The Fall of Reach’
‘Contact Harvest’ (*2524)
‘The Cole Protocol’ (*2535)
‘The Flood’ (novelization of ‘Halo:CE’)
‘First Strike’
‘Ghosts of Onyx’
(*) These two books occur within a time period ‘The Fall of Reach’ glosses over, as the timeframe of that book skips from 2525 to 2552. However because of the background information on the Spartan-II Program and other characters that’s provided in ‘The Fall of Reach’, I highly recommend you read that book in it’s entirety first.
"The Kilo-Five Trilogy" (pre-‘Halo 4′)
‘Glasslands’
‘The Thursday War’
‘Mortal Dictata’
Pre-‘Halo 4′ comic serials
‘Halo: Initiation’ (The story of Sarah Palmer’s recruitment into the Spartan-IV Program and it’s early stages - 6 issues, complete)
Post-‘Halo 4′ comic serials
‘Halo: Escalation’ (Chronicles what has been happening in the Halo Universe after the events of ‘Halo 4′ and Spartan Ops - currently 17 issues, with ongoing monthly releases)
__**__There is also the book ‘Halo: Evolutions’, which contains several short stories scattered throughout the Halo Universe’s timeline.
There are also the fairly new books ‘Broken Circle’ and ‘New Blood’. The first jumps between two different time periods and is all about the formation of the Covenant and it’s early stages, as well as details about the Great Schism. The second is an e-book only, and is about Edward Buck’s transition to becoming a Spartan-IV.
As for other things like terminal videos, ‘Nightfall’, ‘Legends’, etc…a forum member on here (CIA391) has created an expansive and comprehensive list of where practiaclly everything fits into the Universe’s timeline: Halo Canon Order
Hope this helps you out. 