The latest system update for the 3DS (version 5.1) officially adds "further improvements to overall system stability and other minor adjustments." However, users are reporting significant performance improvements in a variety of titles. For example, NeoGAF user Diggeh noticed a more stable framerate in Sonic Generations and Ridge Racer.
Tiny Cartridge pointed out this video of Resident Evil: The Mercenaries 3D, which shows the game before and after the 5.1 update:
We tested a number of games, including Luigi's Mansion, Resident Evil Revelations, and Metal Gear Solid 3D. However, we could not find any appreciable improvement in those games. However, Rayman 3D is significantly enhanced, with much faster load times and a much better framerate--albeit it is still choppy even after the update.
It appears that games that will most benefit from the 5.1 update are games that did not perform great to begin with. Highly optimized games see little difference after the update.
When contacted by Shacknews, a Nintendo representative could not confirm if the update was meant to improve performance, saying they have "nothing to add beyond what was shared." A few have postulated that the 5.1 update could be like the 3.5 update for PSP, which unlocked the full clockspeed of the CPU.