I have to second Soul Hackers, since it's the best port a Saturn RPG could have received, and definitely some of the best fun I've had with the 3DS. The digital version is often on sale for around 5 monies, too (in fact, it's on sale right now in Europe). It takes the series' core gimmick of party-building via demon negotiation and adds the notion of "demon loyalty" to the mix: rather than levelling them up, you increase your demons' loyalty by giving them gifts (e.g. jewels or booze) which in turn makes them more reliable in battle (a neglected demon will often refuse to carry out your orders at the worst possible moment). Apart from learning how to game these systems, if you've played any other dungeon crawlers before you'll be right at home. One of the most impressive things about this port of Soul Hackers is its commitment to the original game's aesthetics. It doesn't just retain the original graphics and music, but as much of the total package as possible, right down to the original compressed-to-hell FMV cutscenes and boss battle transitions, which are all included essentially untouched. The game really nails a specific Gibson-esque conception of cyberspace, and I'm so glad that the 3DS version leaves its specific aesthetic character, its social/political concerns, etc, intact, and doesn't try to awkwardly update them.
I like how off-kilter the gameplay is, too, the demon loyalty system being such that if a boss fight is proving too tough, it's less a matter of levelling up and more a matter of finding the right pals and getting them drunk. The demon dialogue/negotiation is a fair bit more robust than in most of the other SMT games, too. They're still just talking in weird non-sequiturs most of the time, but you haven't exhausted their lines after three encounters. Thanks to this and the trippy nightmare-spaces you encounter them in, the battle situations never get old. I also love the fact that you can hold B to RUN SIDEWAYS DOWN CORRIDORS AT 100MPH - who says dungeon crawlers are 'slow'?