I concur that R-Type 3 is great, though I'll always have a huge soft spot for the original.
Which neatly brings me to my current favourite console for shoot em ups: the PC-Engine/TurboGrafx-16. Best retro device I ever bought... Apart from my Commodore collection, naturally
There's more shoot em ups on the PCE than I can count and there's a couple of
really good ones. The port of R-Type is absolutely
fantastic and Salamander is great too. Blazing Lazers is one of the best non-arcade Shoot Em Ups I've ever played.