Ileum & Ilium

I know, I know. This one will be super-useful on a daily basis. You're welcome.

With an E – part of the small intestine.
With an I – part of the pelvis.

Than & Then

With an A – substance comparison.
With an E – time comparison.

Buy, By, Bye

Buy – Shut up and take my money.
By – Wait, YOU drew this?
Bye – See ya later, alligator.

Moor & More

-oor – (v.) secure a vessel by tying it down.

-ore – (adj.) a larger amount.

Click & Clique

-ck – small, snapping noise.
-que – small, French, snapping noise... No?... OK, it's a group of like-minded people, usually with the implication that they exclude new people from joining.