My favorites... I can only really judge the ones I've played rather a lot of. Unfortunately, I still haven't gotten around to giving some of them the attention they deserve, just because I've got other similar games that gave me a better first impression. Oh, these are all Japanese too, so when I say good value or whatever I'm not sure what TG versions go for.
Cyber Core - pretty standard shooter with one main quirk, but excellent value.
Super Star Soldier - again good value, and a bundle of fun.
Soldier Blade - Possibly my favorite shooter at the moment
PC Genjin - I need to play more of this actually.
Other shooters I own that I haven't played the shit out of:
Aldynes
Gates of Thunder
Dragon Spirit
Parodius
Detana!! Twinbee
Star Parodier
Final Soldier
Aero Blaster (HARD!!!!)
Deep Blue
Gunhed
Salamander
Gradius
R-Type
Galaga 88
And I guess Afterburner II and Space Harrier. And Battle Ace. Do those really count?