These are the causes of death in Nethack 3.3.1 which I found by looking through the source code (apart from being killed by a monster, or a weapon thrown at you).
acidic corpse
alchemic blast
attempting to ride a [petrifying monster]
attempting to saddle a [petrifying monster]
blast of acid
blast of disintegration
blast of fire
blast of frost
blast of lightning
blast of missiles
blast of poison gas
boiling potion
boiling water
bolt of cold
bolt of fire
bolt of lightning
brainlessness
bumping into a boulder
bumping into a door
bumping into a wall
burning book
burning potion of oil
burning scroll
cadaver
carnivorous bag
caught him/herself in his/her own [magical blast]
choking
closing drawbridge
collapsing drawbridge
colliding with the ceiling
committed suicide
contact-poisoned spellbook
contaminated potion
contaminated water
crashing into iron bars
crunched in the head by an iron ball
cursed throne
death ray
deliberately gazing at Medusa's hideous countenance
dragged downstairs by an iron ball
drowned
electric chair
electric shock
elementary chemistry
elementary physics
exhaustion
exploding chest
exploding crystal ball
exploding drawbridge
exploding large box
exploding ring
exploding rune
exploding wand
explosion
fall onto poison spikes
falling downstairs
falling drawbridge
falling object
falling off a [petrifying monster]
falling rock
fell from a drawbridge
fell into a chasm
fell into a pit
fell into a pit of iron spikes
fell onto a sink
gas cloud
gas spore's explosion
genocidal confusion
iron ball collision
kicking [something]
kicking a [petrifying] corpse without boots
killed him/herself with his/her bullwhip
killed him/herself with his/her pick-axe
killed while stuck in creature form
land mine
leg damage from being pulled out of a bear trap
life drainage
magic missile
magical explosion
mildly contaminated potion
molten lava
overexertion
petrification
[petrifying] corpse
[petrifying] egg
poisoned blast
poisoned needle
poisonous corpse
potion of acid
potion of holy water
potion of unholy water
psychic blast
residual undead turning effect
reverting to unhealthy [normal] form
riding a [petrifying monster]
riding accident
rotted [...] corpse
rotten lump of royal jelly
rusting away
scroll of earth
scroll of fire
scroll of genocide
self-genocide
shattered potion
shot him/herself with a death ray
sipping boiling water
sitting in lava
sitting on an iron spike
sitting on lava
slipped while mounting [a monster]
squished under a boulder
starvation
stolen [petrifying] corpse
strangulation
suffocation
swallowing a [petrifying monster] whole
system shock
tasting [petrifying] meat
teleported out of the dungeon and fell to his/her death
the wrath of [deity]
thrown potion
touching [an artifact]
touching the edge of the universe
touch of death
tower of flame
trying to help a [petrifying monster] out of a pit
trying to tin a [petrifying monster] without gloves