These aren't exactly clones, but I think if you enjoy the game play of some of these, then you may enjoy the similar games listed.

The Legend of Zelda (NES) / Golvellius: Valley of Doom (SMS)
Original Metroid Series / Zillion (SMS) / Scurge: Hive (GBA, DS)
Harvest Moon Series / Sheperd's Crossing (PS2) / Innocent Life (PSP, PS2) / Rune Factory (Wii, DS)
Mystic Defender (GEN) / Alicia Dragoon (GEN)
Spy Hunter (arcade, NES) / Action Fighter (arcade, SMS, C64, Amiga)
R-Type Series / Gaiares (GEN)
Tempest Series / Space Giraffe (360)
Radiant Silvergun (SAT) / Ikaruga (DC, GC)
Rygar (arcade) / Black Tiger (arcade)
Kenseiden (SMS) / Samurai Ghost (PCE)
Space Harrier Series / Jinmu Denshou (PCE) / Space Fantasy Zone (TCD unreleased ISO)
Resident Evil 4,5 (360, PS3) / Dead Space Series (360, PS3)
Lumines Series / Gunpey (PSP)
Metal Gear Solid Series / Splinter Cell Series
Ikari Warriors (arcade) / Heavy Barrel (arcade)
Blasteroids (arcade) / Super Stardust HD (PS3)
Smash T.V. (arcade) / Super Stardust HD (PS3)
Kitten Kaboodle (arcade) / Three Wonders: Don't Pull! (arcade)