It's a matter of pain and duration:

Dr No (Boiled alive) | Pain: Incomprensible Duration: Probably a few minutes. Maybe his suit took it longer for him to drown Verdict: Really, really fucking bad

Goldfinger (Sucked out of plane) | Pain: Probably pretty bad when he's getting sucked out Duration: After he's out of the plane he's got a couple of relatively painless (though scary) minutes to live Verdict: Pretty unpleasant, but not nightmarish

Largo (Harpoon through the back) | Pain: Some Duration: About ten seconds Verdict: Tame

Scaramanga (Shot in the chest | Pain: Some Duration: A few seconds Verdict: Very tame

Stromberg (Shot by Bond twice in the groin, once in the chest, and once in the face) | Pain: Quite a bit Duration: About fifteen seconds Verdict: Unpleasant but not horrible

Drax (Sucked into space) | Pain: Decompression has got to be nasty Duration: He's probably dead within a minute Verdict: Quite unpleasant

Kristatos (Throwing knife to back) | Pain: Some Duration: He dies almost instantly Verdict: Very tame

Khan (Plane crashes and instantly explodes) | Pain: Probably none, though it would be scary Duration: Near-instant Verdict: Very tame

Zorin (Falls off Golden Gate bridge) | Pain: Depends on if he died on impact, would be scary regardless Duration: Near-instant Verdict: Tame

Whitaker (Kind of crushed by statue in explosion) | Pain: Some Duration: Near-instant Verdict: Very tame

Sanchez (Lit on fire while covered in gasoline) | Pain: Incomprensible Duration: Only a few seconds since he manages to trigger an explosion that finishes him off Verdict: Very nasty

Trevelyn (Falls about a hundred feet, then gets crushed by giant machinery) | Pain: Quite a bit Duration: Serious pain until the machinery finishes him off Verdict: Quite unpleasant

Carver (Shredded by drill torpedo thing) | Pain: Incomprensible Duration: A few seconds that would feel like years Verdict: Really fucking bad

Carver (Shredded by drill torpedo thing) | Pain: Incomprensible Duration: A few seconds, if he's lucky Verdict: Really fucking bad

Elektra King (Shot in the head) | Pain: None Duration: Instant Verdict: This is the closest a Bond villain can get to dying in their sleep

Graves (Sucked into jet engine) | Pain: If your pain receptors had time to process what was going on, it might be horrible Duration: Near-instant Verdict: Grisly, but probably not painful

Le Chiffre (Shot in head) | Pain: None Duration: Instant Verdict: As tame as it can get

Green (Heatstroke) | Pain: Dying in the desert wouldn't cause blinding pain, but it would be quite a bit of suffering Duration: Hours Verdict: Quite nasty

Silva (Throwing knife to back) | Pain: Considering how much noise he made, a decent amount Duration: About thirty seconds Verdict: Unpleasant but not horrible

FINAL VERDICT: Dr. No was the first, and he still died the worst.