Well, I'm soon going to get a 3DS, but before I get one and start building a 3DS library, I want to make sure I have every good DS game. So take a look at the games I have and recommend me a game I may have missed. I own:

999
Advance Wars x2
ASH
Brain Age 1 & 2
Chrono Trigger
Dragon Ball Z: Attack of the Saiyans
Dragon Quest IV, V, VI, and IX
Final Fantasy III (IV I have for GBA and PSP)
Final Fantasy Tactics A2
Final Fantasy: The Four Heroes of Light
Fire Emblem: Shadow Dragon
Fire Emblem: Mystery of the Emblem (Strongly recommend importing it and playing the English translation)
Front Mission DS
Fullmetal Alchemist
Game & Watch Collection 1 & 2
Golden Sun: Dark Dawn
Infinite Space
Lufia: Curse of the Sinistrals
Mario & Luigi: Partners in Time/Bowsers Inside Story (Plan to Buy)
Metroid Prime Hunters & Pinball
Moon (Plan to Get)
Picross DS and 3D
Planet Puzzle League
Pokemon Conquest
Pokemon HeartGold
Pokemon Platinum
Pokemon Black 1 & 2
Radiant Historia
Sonic Rush
Soma Bringer
SMT: Strange Journey
Starfox Command
Suikoden Tierkreis
Super Mario 64 DS
The Legend of Zelda: Phantom Hourglass & Spirit Tracks

I've bolded all my favorites, keep in mind, I haven't played games like 999, Golden Sun, and Infinite Space yet, so they could be favorites too.

Thanks to your replies, I've added the following games to my "To Buy" list:

Aliens Infestation
Henry Hatsworth (Considering it)
Pheonix Wright 1-4 + Investigations (going to try it before I get it for sure)
Prof Layton 1-4

I even found a guy on ebay who offers the Prof Layton Series for cheap

I'm not interested in the following

Dementium 1 & 2
Dragon Quest Monsters
Final Fantasy Crystal Chronicles
Kingdom Hearts
New Super Mario Bros.
Shin Megami Tensei games
Sonic: Dark Brotherhood, or any more Sonic games
The World Ends With You

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The reason I ask is because I was tried out my friends copy of Bowsers Inside Story based off recommendations from people on the forum, and while trying it, I remembered Moon, which I have played before, and loved (It's literally Metroid Prime, but on the Moon). While I have every highly rated game, not all good games are highly rated (e.g. Front Mission), and I feel like I may have missed others.

Is The Dark Spire any good?

Bare in mind, I can't own every half decent DS game. As it is, I have 15 games on my backlog, plus 20 games for PSP (only got PSP 1 year ago). I need time to play the great 3DS games too, so only recommend me really good games.

I find the lack of Phoenix Wright DISTURBING.

I don't see any of the three Etrian Odyssey on your list.

You don't have The World Ends With You?!  Turn off your computer and go get it right now!

I played that game for 3 hours, tried to like it, but I just don't. I don't like modern era/emo/ whatever you call it JRPG's (SMT falls in the same category).

I never played Pheonix Wright, or Professor Layton....guess I should try out those games too. Which one should I try first, to judge the series?

As for Etrain Odyssey, I don't like Dungeon Crawlers. The only DC I ever enjoyed was Soul Blazer for the SNES.

How did you not play Dragon Quest Heroes: Rocket Slime with that much love of Dragon Quest on your list. It's a nice little gem that you will like. Get Mega man zero collection too I love those GBA games and all 4 are on 1 nice cart. Aliens Infestation is another amazing masterpiece from Wayforward. Ninja Gaiden Dragon Sword is super fun but is not for everyone and to end this post for now Henry Hatsworth and the puzzling adventure is just smashing. All of those games are great action/adventure goodness.

The first one of both. Ace Attorney and the Curious Village.

The Dark Spire is awesome, if you can get your hands on one copy, don't waste time and get it. I know you said you weren't interested in any FF Crystal Chronicles recommendations, but there's no way I wouldn't recommend you Ring of Fates. Seriously, it's IMO, the best JRPG from the DS, probably my favourite RPG from the last gen. BUY IT! Anyway, other games I would recommend you:

Megaman Zero Collection
Megaman ZX/ZX Advent
Phantasy Star Zero
Sands of Destruction
Castlevania Portrait of Ruin/Dawn of Sorrow
Rune Factory
Tales of Innocence(if you can read japanese)
Pokémon Ranger
Pokémon Mystery Dungeon
Another Code
Contra 4
Disgaea DS

FF XII Revenant Wings

And that's the ones I remember. Too many games on DS's library.

I did miss something, Aliens Infestation! That looks just like Metroid Fusion, I love it...

...oh boy, I thought I had it all for DS....

Megaman Zero Collection looks great, but like Sonic it's just too many games. I love Megaman, but I can only handle so much. So I pretty much avoid Sonic, Megaman, and Super Mario Bros. Platformers. It's pretty much the same formula for 20+ years now.

As for Dragon Quest....thing is, I actually haven't played any of them on the DS. LOL, I love Retro Final Fantasy's and I've played a good amount of Draqon Quest VIII on PS2, so I bought these planning on playing them when I get a 3DS XL and take advantage of the larger screen. DQ IX and Golden Sun are 2 of the first DS games I plan to beat when I get a 3DS XL. So the reason why DQH:RS isn't on my list is because I have enough DQ.

I played Ninja Gaiden, it's pretty good, but I don't really want to own it. Not a fan of hack and slash.

As for Henry Hatsworth, I'll look into it. Which is better Hatsworth or Professor Layton?

Do you have Chrono Trigger on a different platform?