I was just skimming through my backup and had that in my mind after comparing my original discs with the GOG version, but I'll go through once more more thoroughly. Should not be an offensive, I originally had the Larry, Might & Magic and Wizardry games in my head that they had some missing stuff (PlaySpy, missing hint books and the manual from The Ultimate Wizardry Archives). To my delight, all is here :)
So no "missing content" alarm then? :)
I went through my collection and was comparing, a manual should accompany every game, rest like hint book or soundtrack is fair game and in my eyes not mandatory :)
These games do have these missing things in their original release:
Age of Wonders: missing manual
Age of Wonders 2 - The Wizard's Throne: missing manual
Age of Wonders 2 - Shadow Magic: missing manual
Brütal Legend: no soundtrack, missing manual
Crusaders of Might & Magic: missing manual
Darkstone: after release, there were some extra offical quests, tools and skins (and tools), see , , )
Deathtrap Dungeon: Audio tracks are missing from the original CD
Deponia 2: Chaos on Deponia: missing manual
Deponia 3: Goodbye Deponia: missing manual, missing soundtrack (there is an extra audio CD in the physical release)
Desperados 2: missing soundtrack (unsure, Desperados 1 has one)
Edna & Harvey: The Breakout: missing manual
Edna & Harvey: Harveys new eyes: missing manual
Gabriel Knight - Sins of the Fathers: missing graphic novel, missing hintbook (see below)
Gone Home: missing soundtrack and extras of the "collectors edition", see their webpage.
Gray Matter: missing manual, missing soundtrack, missing postcards, missing card game.
Jagged Alliance - Deadly Games: missing manual
Kings Quest 1,2,3: missing hintbooks
Kings Quest 4,5,6: missing hintbooks
Kings Quest 7,8: missing hintbook for 7, dunno if for 8 a sierra one exists
Leisure Suit Larry 7 - Love for Sail: maybe there is a sierra hintbook, if yes, it's not here
Mega Race 1+2: missing manuals
Might & Magic 8 - Day of the Destroyer: missing map
Moto Racer: missing soundtrack / audio tracks
Moto Racer 2: zero extras! at least manual please :)
Omikron - The Nomad Soul: maybe missing audio tracks (unsure)
Pandemonium: zero extras! missing manual + missing soundtrack / Audio tracks
Pandemonium 2: missing manual + missing soundtrack / audio tracks
Patrician 1+2: missing manual for Patrician 1, missing map for Patrician 2
Personal Nightmare: missing manual
Police Quest 1+2+3+4: missing hintbooks
Police Quest SWAT 1+2: missing manual for PQ-SWAT 2
Populous - The Beginning: missing audio track/soundtrack
Quest for Glory 1-5: missing hintbooks for 1-4, dunno if Sierra made one for 5
Realms of Arkania 1+2: missing overworld maps, soundtrack for 2 is not the real one ..., including the German manuals would be awesome.
Realms of Arkania 3: German manual would be awesome, soundtrack is not the real one ...
Rise of the Triad: missing manual
Screamer 2: missing manual
Silent Service 1+2: missing map for 1 (unsure)
Space Quest 1+2+3: missing hintbooks
Space Quest 4+5+6: missing hintbooks
The Book of Unwritten Tales: missing soundtrack, missing artbook, missing manual
The Book of Unwritten Tales - Critter Chronicles: missing soundtrack, missing artbook, missing manual
The Night of the Rabbit: missing soundtrack, missing manual, missing audiobook "Mauswald"
Theme Park: missing manual
Tiny and Big Grandpas Leftovers: missing soundtrack
Torins Passage: missing hintbook
Ultimate Body Blows: missing manual
Unreal Tournament 2004: the community bonus packs / maps  would be really neato
Wing Commander 5 - Prophecy: "Secret Operations"DLC is missing, see 
For the nearly every Sierra game there are official hintbooks available, see .
These games might have had some sort of printed instructions which are not included (yet), but due to their shareware nature, I'm not really sure:
Catacombs Pack, Secret Agent, Tyrian 2000 (original Tyrian as an extra would be neat)
It would be nice though, to provide for every game a box art picture for the windows explorer (folder.jpg) in a decent resolution (ie height 256 or 512 pixels).