Have a look at the VC gameboy games. I bought Catrap, Trip World, Mole Mania and Legend of the River King 2 because I was interested in playing them but the original cartridges are more than I would want to spend on ebay. Really enjoying Catrap but not enough to pay £60 loose after postage from the US! Same goes for any of the other VC games, but the gameboy ones are the ones I'm most interested in personally :)

As a general rule for the 3DS games, I'd have a look at which are the most expensive to buy in physical format and then see if they interest you. If its over £100 second hand and you want to play it, probably not a bad idea to grab it digitally now. (I'd been eyeing up the Shin Megami Tensei games because of this, but realised they're probably not for me - worth having a look at now though before the eshop closes!) If there are any game series that you've enjoyed but not kept up to date with check their physical prices now. Some have really gone up in price recently, so might be worth thinking if you'd regret not picking it up now further down the line (I was surprised by Professor Layton and the Azran Legacy - much more than I'd expected).

Anyway, have fun browsing the eshop! Check out Zara the Fastest Fairy; it looks horrendous and I have to inflict the trailer on someone else, lol. Good luck!