perhaps you could try time hollow.
in the game you have to check places all over "town" (you get a 2D map, from where you can enter an "area" which is a sort of 2d panoramic view of a room/street where you can check stuff/people by tapping them)
when you have enough clues regarding certain events you can open a hole in time, and change something in the past to completely change the present(opening up new mysteries)

another one is "another code: 2 memories"(trace memory for the US release)
which is 3D viewed mostly from the top.
here you not only have to find clues, but also solve some actual puzzles(not as in figuring out events, but real puzzles presented as puzzles)
stuff like placing objects in a certain order opening up secret doors.

both aren't really long, but are worth it.

phoenix wright isn't really like what you want i think.
it's first finding some clues, and then enter a wacky discussion with another attorney, a judge, and crazy witnesses, to figure out who committed a crime(or who didn't).
but you should still give it a try, certainly a lot of content available in the PW series.

 

Update: Played and beat Time Hollow. Totally recommend it. Post credits gave me chills. Sill taking recommendations

 

You might wanna try Hotel Dusk: Room 215.

 

Watch out for Lux Pain. It has a good story and would be a decent game if the company that localized it could have gotten their crap together and made an effort. The text has tons of errors, what is printed on the screen does not actually match what the character is saying in-game. It could have been an amazing game if the editors and translators, even QA could have agreed on at least the spelling of the characters names.

Also you can try Theresia, Dear Emile. It's pretty creepy, has a decent story, actually 2 stories, but it does have the pixel hunting problem. Sometimes it's hard to see what you're supposed to click on with the stylus. Also it's interesting that you need to find elixirs to heal because you can take damage in the game.

 

sooo.....do we recommend point n' click adventure games now?

broken sword
runaway 2,3
so blonde

 

The EU version of Lux Pain has most of the typos fixed, I thought it had a great story and good writing too, it was just let down by some poor choices in game progression.

 

Maybe try Again? It's from the makes of Hotel Dusk. I haven't had time yet to play it myself, but it does look interesting, it seems like you have to compare places from the past (crime scene?) and from the time you're in.

And have fun with Lux-Pain! I really liked the game and it's one of my favorite stories. In the beginning I hated it that what they say isn't the same as the text and I thought the voice acting was quite bad, so undubbing is recommended (those voices I did like!)~! Just a tip: try out both the normal and good end, cause both endings are good~!

EDIT:
+1 for Lone Wolf, wish they would port more.

Also if you just want a good story, (yes I know it isn't ARG), you could take a look at vnds, it's a homebrew that can play visual novels, quite a few good ones have been ported already. (Tsukihime, FSN) If you don't like VN's (or maybe played them on the pc already) then just ignore this xD

 

You could also look here: http://vsrecommendedgames.wikia.com/wiki/Nintendo_DS
They give quite a few good recommeded games. Because of that I have about 15 more games on my Acekard now xD

And yes, VNDS can be troublesome sometimes. Just yesterday I was playing FSN and suddenly I didn't hear the voices anymore, I put it on my pc to fix it, but when I put it back I somehow missed bits of the script. It took me the whole of today to get the game running again (downloaded everything again and followed someones steps. Now I can finally finish it~!