EDITED: May 25th, 2013Time for me to  

  my bookshelf. Sorted by series, then by chronology of the universe: (Notes may have spoilers)
The 39 Clules: One False Note 
Good for a Book 2The 39 Clues: Into the Gauntlet 
Great endStargate: Atlantis - Legacy - Homecoming 
Was okayFace of the Deep: The Word Reclaimed 
Enough future history for me, great ship-to-ship battles and politics to keep me interested. Excellent bookRobot Wars: Death Trap 
GreatRanger's Apprentice: The Ruins of Gorlan 
GreatThe Underland Chronicles: Gregor the Overlander 
It was good.The Quest for Truth: Taken 
GreatThe Quest for Truth: Risk 
GreatStar Trek: Enterprise - Broken Bow 
Novelization on the pilot, pretty good.Star Trek: Enterprise - What Price Honor? 
Okay, except for a handful of glaring continuity issuesStar Trek: Enterprise - Rosetta 
GoodStar Trek: Enterprise - The Good That Men Do 
Excellent set-up for Kobayashi Maru and the Romulan War miniseriesStar Trek: Enterprise - Kobayashi Maru 
ExcellentStar Trek: Enterprise - The Romulan War - Beneath the Raptor's Wing 
Except for occasional use of language and a few pages conflicting with my beliefs, it was good/greatStar Trek: Vanguard - Harbringer 
Good first book in a seriesStar Trek: Vanguard - Reap The Whirlwind 
Really didn't catch my attention in terms of keeping my interest as the first book did.Star Trek: Vanguard - Open Secrets 
GoodStar Trek: The Next Generation - The Valiant 
GreatStar Trek: Section 31 - Deep Space Nine - Abyss 
Great continuation of the DS9 "Relaunch" and keeping with the nature of the book being a part of the Section 31 miniseriesStar Trek: Section 31 - Shadow 
GoodStar Trek: A Time To Die 
2nd book in a series of 2-book-2-parters, and does it quite wellStar Trek: Gateways - What Lay Beyond 
ExcellentStar Trek: Mirror Universe - Obsidian Alliances 
BLECHStar Trek: Titan - Taking Wing 
Great tie-in to Nemesis, taking place a bit before the final few scenes of the movie and also being an "extension" of the movie itselfStar Trek: New Frontier - Treason 
1st of the typical "2-parter books" that New Frontier is made up of, would be an okay 1st part to what could be the last book of New FrontierStar Trek: New Frontier - Blind Man's Bluff 
Haven't read it yet, possible end of New FrontierStar Trek: The Next Generation - Resistance 
Great story, though parts of it made me question if this would have made it as an episodeStar Trek: The Next Generation - Greater Than The Sum 
Excellent, managing to focus on one character's development while making it a good sequel to Before Dishonor and Resistance.Star Trek: Destiny - Gods of Night 
Great beginning to a trilogyStar Trek: Destiny - Lost Souls 
Excellent ending, while opening it up for the Typhon Pact miniseriesStar Trek: Destiny 
The three Destiny books all in one, so I finally could read Mere Mortals. All together, amazingStar Trek: Department of Temporal Investigations - Watching the Clock 
Great temporal story, excellent conclusion to the TCWStar Trek: A Singular Destiny 
Great continuation of the Destiny trilogy, while planting seeds for Typhon Pact.Star Trek: Titan - Synthesis 
Good/great story, mixing elements of ship-to-ship combat, diplomacy, engineering, and exploration to keep my interestStar Trek: Voyager - Full Circle 
Great start to the Full Circle Fleet storylineStar Trek: Voyager - Unworthy 
Great. Character interaction as well as the Fleet project itself went wellStar Trek: Voyager - Children of the Storm 
Had no idea this would be the pre-finale to the Full Circle Fleet storyline. Great continuation of David Mack's Children of the Storm from Destiny's Mere Mortals.Star Trek: Voyager - The Eternal Tide 
Haven't read it yet, end of the Full Circle Fleet storylineStar Trek: Typhon Pact - Seize The Fire 
While losing my interest wholly when I originally read it, I finally read through it a few months later, while sustaining a "I-just-want-to-see-how-it-ends" feel.Star Trek: Typhon Pact - Rough Beasts of Empire 
Excellent story, especially on the political side of thingsStar Trek: Typhon Pact - Paths of Disharmony 
Okay/Good Andorian storyline, good tie-in to Vanguard, good political/Earth focus, great/excellent Picard family situation and Chen's assistance in that regardStar Trek: The Next Generation - Indistinguishable From Magic 
I thought it absurd to jump ahead 2 years of what most of the other Destiny Star Trek writers were writing, and it turned out that I was right. While the story was excellent, the endgame and time jump to 2 years ahead ruined it for meStar Trek: Cold Equations - The Body Electric 
Great endingStar Trek: Myriad Universe: Infinity's Prism 
All 3 stories in it are great/excellentGraphic Novel/Comic:
Star Trek: The Modala Imperative 
Okay/GoodSeparate chronology:
Star Trek: Online - The Needs of the Many 
Like it now, but still likes the Destiny universe betterNon-fiction:
The Star Trek Encyclopedia, 1994 edition 
The first of three editions, I believe...Star Trek: The U.S.S. Enterprise Owners' Workshop Manual 
Awesome source for what I call "Half-canon", details belowThe Making of Star Trek: Insurrection 
Nice source, good to see how the movie came together, and why the movie went in the direction it did.PC Gamers Magazine, May 2002 
My sis picked it up for the Star Trek game inside, pretty goodTimeline of War: From Early Weaponry to Weapons of Mass Destruction and Beyond 
Not read yetStar Trek: Star Charts 
Used in the Destiny timeline, haven't read yetMy usual classification of rating: (Along the lines of the following)
Lousy/BLECH
Poor
Okay
Good
Great
Excellent
Amazing
My classification of canon:
Canon: What is considered canon in that universe, i.e. Star Trek does TV and movies, I believe, as does Stargate.
Half-Canon: What I call the tie-in merchandise or whatever, like Star Trek's Countdown 2009 and Countdown to Darkness comics, which have no contradictions and are stated to be "canon" (Yes, I know that means nothing, but it usually means the content fits what actually is canon)
Non-canon: Even licensed products, like Star Trek's 
Star Trek Online and the Destiny universe books, are non-canon.