aweigh
Are you sure about the Retroarch version? It's currently at 1.5.0, with a planned 1.5.1 coming soon... even the nightlies are still at 1.5.0.
Try using this shader for PPSSPP (don't use the Retroarch PPSSPP core, it's very old and outdated, use the standalone emulator):
http://nix.moderatelyimpressive.com/shaders/arcadescanlines1.1.zip
I use preset "2" for 2d games. I don't use it for everything, though... here's an example of Tactics Ogre:
As for Retroarch shaders, CRT-easymode and CRT-hylian are decent, with easy parameters to set. There's one shader I'm very fond of, it's called GTUv50, but it's not for everyone. It's got some nice dithering solutions and resembles a rather soft CRT.
The Desmume core in Retroarch seems fucked up because I couldn't find the SoftRasterizer/OpenGL toggle - that means no map in Dark Spire, for example. I use the standalone version.
That said, I wouldn't use CRT shaders when emulating NDS and other portable systems though - Retroarch has specific LCD shaders which feel much more genuine for those systems (some of them even simulate the native ghosting of the systems' screens, but I never use that). The one I recommend is LCD-grid v2, under the "handheld" shader folder.
Here's an example of Circle of the Moon (GBA):
LCD-gridv2 (you can adjust the intensity of the grid):
GTUv50:
Here's a screenshot of Gradius Gaiden (PSX) running with GTUv50:
Bonus
I love Retroarch because it's got very little input lag and much better video timing than pretty much every standalone emulator out there. However, some cores aren't great on it. It's not great for PSP and NDS, which unfortunately seem to be your primary interest. It's great for just about everything else, though...