Just for the sake of comparison and possibly to jog the memories or votes of people who haven't posted yet, here is the shmups.org 2012 thread for best shooters of all time.
Top 25
01. Battle Garegga (AC/SAT)
02. Mushihimesama Futari / 1.5 / Black Label (AC/360)
03. Ketsui ~Kizuna Jigoku Tachi~ (AC/360)
04. DoDonPachi Dai-Ou-Jou / Black Label (AC/360/etc.)
05. Armed Police Batrider (AC)
06. DoDonPachi (AC/SAT/PSX)
07. Batsugun / Batsugun Special (AC/SAT)
08. Raiden Fighters Jet (AC/360)
09. ESPGaluda (AC/PS2)
10. Mars Matrix (DC/AC)
11. Mushihimesama (AC/PS2/360)
12. Gunbird 2 (AC/DC)
13. ESPGaluda II (AC/360)
14. Radiant Silvergun (AC/SAT/360)
15. Dragon Blaze (AC/PS2)
16. Strikers 1945 II (AC/SAT/PSX/PS2)
17. R-Type (AC/PCE//PSX/etc.)
18. Ikaruga (ARC/DC/GC/360)
19. Giga Wing (AC/DC)
20. Battle Bakraid (AC)
21. Soukyugurentai / Terra Diver (SAT/AC/PSX)
22. Ibara (AC/PS2)
23. DoDonPachi Daifukkatsu/1.5/Resurrection (AC/etc.)
24. Muchi Muchi Pork! (AC/360)
25. Gradius Gaiden (PSX)
Honourable Mention
Akai Katana / Shin (360/AC)
Blazing Star (AC/NG)
Cho Ren Sha 68K (PC/X68)
Crimzon Clover (PC)
Cyvern: The Dragon Weapons (AC)
Dangun Feveron (AC)
Darius Gaiden (AC/SAT/PS2/etc.)
Deathsmiles / Mega Black Label (AC/360)
Dimahoo / Great Mahou Daisakusen (AC)
DoDonPachi Daifukkatsu Black Label (AC/360)
DonPachi (AC/SAT/PSX)
Einhänder (PSX)
Eschatos (360)
ESP Ra.De. (AC)
Fire Shark / Same! Same! Same! (AC/GEN)
G-Darius (AC/PS2/PSX)
Gradius II: Gofer no Yabou (AC/SAT/FC/etc.)
Gradius V (PS2)
Guwange (AC/360)
Hellsinker (PC)
Imperishable Night [Touhou 8] (PC)
Perfect Cherry Blossom [Touhou 7] (PC)
Pink Sweets ~Ibara Sorekara~ / Arrange (AC/360)
Progear no Arashi (AC)
R-Type Delta (PSX)
Raiden DX (AC/PSX)
Raiden Fighters 2: Operation Hell Dive (AC/360)
RayForce/Layer Section/Galactic Attack/Gunlock (AC/etc.)
Recca [Summer Carnival '92] (FC)
Strikers 1999 / Strikers 1945 III (AC)
Thunder Force III (GEN/MD/SAT)
Thunder Force IV / Lightening Force (MD/GEN/SAT)
Twin Cobra / Kyukyoku Tiger (AC/PCE/etc.)
Undefined Fantastic Object [Touhou 12] (PC)
Under Defeat (DC/AC)
I'm suspecting that I may prefer that list to the results which will come here.
Top 25
01. Battle Garegga (AC/SAT)
02. Mushihimesama Futari / 1.5 / Black Label (AC/360)
03. Ketsui ~Kizuna Jigoku Tachi~ (AC/360)
04. DoDonPachi Dai-Ou-Jou / Black Label (AC/360/etc.)
05. Armed Police Batrider (AC)
06. DoDonPachi (AC/SAT/PSX)
07. Batsugun / Batsugun Special (AC/SAT)
08. Raiden Fighters Jet (AC/360)
09. ESPGaluda (AC/PS2)
10. Mars Matrix (DC/AC)
11. Mushihimesama (AC/PS2/360)
12. Gunbird 2 (AC/DC)
13. ESPGaluda II (AC/360)
14. Radiant Silvergun (AC/SAT/360)
15. Dragon Blaze (AC/PS2)
16. Strikers 1945 II (AC/SAT/PSX/PS2)
17. R-Type (AC/PCE//PSX/etc.)
18. Ikaruga (ARC/DC/GC/360)
19. Giga Wing (AC/DC)
20. Battle Bakraid (AC)
21. Soukyugurentai / Terra Diver (SAT/AC/PSX)
22. Ibara (AC/PS2)
23. DoDonPachi Daifukkatsu/1.5/Resurrection (AC/etc.)
24. Muchi Muchi Pork! (AC/360)
25. Gradius Gaiden (PSX)
Honourable Mention
Akai Katana / Shin (360/AC)
Blazing Star (AC/NG)
Cho Ren Sha 68K (PC/X68)
Crimzon Clover (PC)
Cyvern: The Dragon Weapons (AC)
Dangun Feveron (AC)
Darius Gaiden (AC/SAT/PS2/etc.)
Deathsmiles / Mega Black Label (AC/360)
Dimahoo / Great Mahou Daisakusen (AC)
DoDonPachi Daifukkatsu Black Label (AC/360)
DonPachi (AC/SAT/PSX)
Einhänder (PSX)
Eschatos (360)
ESP Ra.De. (AC)
Fire Shark / Same! Same! Same! (AC/GEN)
G-Darius (AC/PS2/PSX)
Gradius II: Gofer no Yabou (AC/SAT/FC/etc.)
Gradius V (PS2)
Guwange (AC/360)
Hellsinker (PC)
Imperishable Night [Touhou 8] (PC)
Perfect Cherry Blossom [Touhou 7] (PC)
Pink Sweets ~Ibara Sorekara~ / Arrange (AC/360)
Progear no Arashi (AC)
R-Type Delta (PSX)
Raiden DX (AC/PSX)
Raiden Fighters 2: Operation Hell Dive (AC/360)
RayForce/Layer Section/Galactic Attack/Gunlock (AC/etc.)
Recca [Summer Carnival '92] (FC)
Strikers 1999 / Strikers 1945 III (AC)
Thunder Force III (GEN/MD/SAT)
Thunder Force IV / Lightening Force (MD/GEN/SAT)
Twin Cobra / Kyukyoku Tiger (AC/PCE/etc.)
Undefined Fantastic Object [Touhou 12] (PC)
Under Defeat (DC/AC)
I'm suspecting that I may prefer that list to the results which will come here.