Though, I have been questioning lately whether a 16 gig card will do you any good in a 3DS, since there MAY be a hard limit on the number of downloads, regardless of file size, that you can have on your 3DS home menu (see thread http://www.nintendoworldreport.com/forums/index.php?topic=36488.0)
Uncle Bob, it seems, has discovered that there is a hard limit, at 300. While the 3DS can support a maximum 32 gigs in an SD card, I'm not sure if it can ever actually use that much space. Maybe not even 16, because that's what I've got in my 3DS right now, I've got about 90 apps/icons right, and I have 106, 362 open blocks. The largest game I have is Mighty Switch Force, which is 1617 blocks. But I don't think that'll be the norm for eshop games, because Freaky Forms is less than 300 blocks and Pushmo is less than 200. The average GB game is 30 odd blocks, GBC is 40 odd, and none of them ambassador games, GBA or NES, are over 80.
Now according to my good friend Google, 1 gigabyte equals 8000 blocks and change (128 kb equals 1 block). So let's say you just went to an 8GB SD in your 3DS. You would have over 65,000 blocks to fill up, which means you can buy at least 40 games that are as big as Might Switch Force, or 1800 GB games, or 1400 GBC games, etc. etc. Obviously, you will buy a combination of all of these, but unless you're one of those crazy people who worries about running out of icon space on your home menu and starts forum threads about them (i.e. ME), I doubt you will every use up 8gb, much less 16. And how in the world would you use up 32GB, that is beyond me.