heavy, loud, resounding
dull, muffled, soft
sickening

give
She felt her heart give an extra thud.

make
The boot made a dull thud as it hit the ground.

hear
feel

with a thud
He hit the floor with a sickening thud.

the thud of a heart, the thud of hooves

hard, painfully, wildly (all only used with heart)
Her heart thudded wildly inside her chest.

heavily, loudly

against
The waves thudded against the side of the ship.

into
The sniper's bullets thudded into the wall.

on
Steps thudded on the stairs.

with
His heart thudded with excitement.

Thud is used with these nouns as the subject:
heart