DS/3DS:
Infinite Space. Visual novel meets space combat, niche game but one of my favorites. Hard to find though so you'll most likely have to emulate it.

Black Sigil: Blade of the Exiled. Very Chrono Trigger-esque RPG, from the battle system down to dual and triple techs. It is slightly glitchy though and it will crash from time to time, but if you save often it's not that big of a deal.

PC:
Septerra Core. Older RPG, has a console feel to it despite it being developed for PC. Graphics and animations are dated but the story is solid and there's a lot of character interaction with each other and NPCs.

Evil Genius. Villain simulator, build your own secret base and hire henchmen and supervilains to work for you. It's really hard to describe how fun it is, think of it like The Sims meets Dr. Evil.

Space Pirates and Zombies. Homeworld in 2D, with a sense of humor and customizeable ships.

Starpoint Gemini. 2.5D space sim, with light RPG elements.This is one of my favorites, it's hard to describe so the best thing I can say is look it up on youtube.

Starpoint Gemini 2. Totally different game from SPG most notably being full 3D. Some gameplay elements are simplified though, the skill system and ship equipment being most notable. If you're a fan of games like Freelancer or Wing Commander: Privateer you'll probably like it.