Colonel & Kernel

I know what you're thinking; but I wasn't gonna shill for some fast food restaurant here...

Regimen & Regiment

Without a T – a course of activity, such as a medication or exercise schedule.
With a T – a military unit.

Stalking & Stocking

These two don't sound quite the same, at least in my ears. But they're pretty close, and they were my son's suggestion. So I've been saving them for the holiday season, y'know? ;)

Gorilla & Guerilla

My all-time favorite homophone! I remember giggling about this in junior high with my friend Abe so much that we got in trouble with a librarian. :)
I suppose, looking back, it's not that funny, really. It's also a lazy anglicization of a Spanish word, so you could make the argument that these really aren't homophones at all. If you wanted to be that way.

Breach & Breech

With an A – (v.) break through from one area into another.
With an E – (n.) hind section of an object or animal.

Slay & Sleigh

I hear the NRA can't make up their mind whether to endorse hunting Santa's reindeer or arming Santa to protect them. I'm sure it will all work out...
Happy holidays!

Ordinance & Ordnance

With the i – a rule or law.

Without the i – military weapons and ammunition.

Pistil & Pistol

-il – the ovule/seed-producing reproductive organ of a flower. Named for its resemblance to a pestle.
-ol – handgun; though sometimes defined as a subset of handguns in which the chamber and barrel are integrated into a single unit. Of course, if you find someone willing to nitpick this point with you, that's probably a discussion you should back slowly away from.