constant, deep (figurative), dull, nagging, throbbing
familiar
muscular, stomach, tummy

be aware of, feel, have
She kept feeling the nagging ache in her heart.
I felt the familiar ache in my lower back.

ease
He changed his position once again to ease the ache in his back.

throb
A dull ache throbbed at the back of David's head.

ache in
a nagging ache in her knee
She could hardly speak for the ache in her heart.

ache inside
ache of
the ache of loneliness inside him

aches and pains
He was always complaining about his various aches and pains.

badly, really, terribly
My feet ached badly.

a little, slightly, etc.
My left foot ached a little.

from
I still really ache from all that running yesterday.

ache all over
Her head felt hot and she was aching all over.

Ache is used with these nouns as the subject:
back, body, chest, ear, head, heart, joint, knee, leg, lung, muscle, neck, side, throat, tooth, tummy