UPDATE: The answer is "No". So far we have not been able to notice any enhancements to the game when played on a 3DS system.
You may read the following article knowing that it was written prior to the 3DS release:
-------------------------------------- N+ --------------------------------------I was getting ready to do a very large post that would outline all the reasons I believe that Pokemon: Black and White versions will have 3DS enhanced visuals and features. But luckily during a mail-bag session of questions from IGN to Nintendo, Nintendo had pretty much said what we needed to hear:
CAN I PLAY MY OLD GAMES?
A. The 3DS will be backwards compatible with all DS and DSi games. Those games will not be able to display imagery in 3D despite being used on the 3DS. However, some games, most notably Pokémon Black & White, will gain some enhanced functionality when played on the new system. These cases should be considered extremely rare, however.
It's pretty dang important to note thought that part of this quote has now been removed from
where they posted it. Either because they made some stuff up, Nintendo realized that they were not supposed to give that much information out and asked them to "forget" that part, or some other reason. They also included an image showing a thumbs-up (

) over Pokemon Black, as well as some other games... does this graphic simply state that these games will run? or that these three games specifically will have added features or 3D depth?

Now as far as what the Pokemon games get in the added features (if fact), I can't find anything anywhere where Nintendo may have said what they are. I can tell you MY thoughts though, as I have played through the main story of the game, all the way through the Elite Four and entering the Hall of Fame on my Japanese Black version:
3D Visuals:When battling, the camera moves in deep, and far out for different attacks, it also pans left and right and up and down, it just goes all over the place, and if you sit idle for long enough the camera "gets bored" and drifts around aimlessly. This to me is a clue to being a "fun" little action when enabled with 3D visuals, and kind of pointless when there are no 3D visuals. Also attacks that have "spray" effects to them like water blasts or fire blasts or drifting leaves, also seem to be designed in more of a back to front or front to back (depending on being attacked or attacking) perspective, and would only be enhanced with 3D to make more sense, however with 3D off it still gives a good illusion of depth, so maybe this could be just a good trick to look better IF 3D enhancment is NOT real.
When you are getting "info" on one of your monsters, the data: abilities, attack, Original Trainer, etc, are displayed on the top screen as always, but inside a more complex visual design, that looks to me, like it has more layers - again if 3D were turned on this would give stronger reason to the "layer" look of the data pages.
World ares have many forced perspective changes. The camera gets very low in certain areas like walking through the huge city, over the long very large Golden Gate like Bridge, as well as other areas that would benefit greatly with 3D enhanced depth, as well as times when the camera gets VERY far away from your character, one time specifically I remember is walking across a very long bridge and the camera went very far up in the sky to go OVER the "tips" of the bridge structures that hold the cables for supporting the bridge, something that would look VERY cool in 3D, and is to a small degree a little pointless in 2D.
Hardware / Software FeaturesSpot Pass functionality is screaming in my ears when thinking about the "Dream World" you have online. You may be able to have the dream world be affected every time the 3DS comes across a WiFi signal. Street Pass is an easy function to change the whole "Black City" vs "White Forest" areas that are exclusive to each game. When players interact with each other using the "High Link" feature, the other persons City / Forest gets changed somehow, and why not make it go the extra mile with these "Pass" features?
A pedometer built right into the 3DS can totally expand the poke-walker functionality of counting steps to help with some in-game goodness. It could help Pokemon who need certain affection levels to evolve get to that state with much more ease. Or how-about hatching an egg?
These are just some of the things that caught my eyes while playing through the game myself, and I was even thinking about all this WHILE I was playing through, well before the rumors even went around the web. Almost every step of the way I felt like I was playing a game ready for 3DS. Also just look at the CRAZY launch timing of what could be the biggest release of a new Pokemon RPG since Red and Blue. Depending on your region in the world the Pokemon games come out DAYS before the new system. I doubt Nintendo would try to instantly make Black and White obsolete games.
Do you remember the original Gold and Silver games? most people remember them as Gameboy Color games, but they weren't. Oh no, they were regular old Gameboy games that got full GBC functionality, Crystal was the "Only For Gameboy Color" game! The infrared port, and the amazing color palette were used with Gold and Silver! Some people may argue that all Gameboy games had color when played on GBC because they were designed with the Super Gameboy for SNES in-mind, and while that's true, NON of them could match the amazing palette of Gold and Silver, and certainly not with that many colors on the screen at once. Those games were made for GBC, but released so that Gameboy owners could play too, WITHOUT adopting a new system right away. Yes, it makes perfect sense that Nintendo should 3DS enhance Black and White, you get ALL of the current DS model market to play to, as well as having a "Killer App" for your new device for early (and late) adopters as well.
I know that some people have been on the fence about the 3DS' "launch window" and weather or not they should get one right away. I think that if Pokemon is 3DS enhanced, many of those fence-sitters will jump into the new yard and get one right away. What about you? do you think that these games are or are not enhanced on 3DS? were you on the fence about 3DS, and now feel differently? Tell us in the comments!