Regimen & Regiment

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

Bough & Bow

-ough – tree branch.
-ow – (v.) bend formally at the waist. (n.) the front end of a ship.
But remember not to confuse these kinds of bows with these kinds of bows!

Pendant & Pendent

With an A – (n.) a hanging ornament, such as a piece of jewelry.
With an E – (adj.) describing something in the act of hanging, like a pendulum.
So, yes, by definition pendants are pendent. I know, it's confusing. And remember not to confuse them with a pennant, either.
Good luck!

Marshal & Martial

John Wayne vs. Ralph Macchio

Die & Dye

Coroner: The victim's lungs appear to be filled with hair coloring.
Detective: What happened to him?
Coroner: He dyed.

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? ;)

Rye & Wry

Flew, Flu, Flue

Trying my darndest to come up with a bird flu / bird flew joke here, but I just can't pin one down. Maybe you can? Leave it in the comments!

Chews & Choose

He chooses, he chews. 

You choose, you chew.

Shear & Sheer

Tort & Torte

Our lawyer dude is back again, this time with some sort of legal injunction against the deliciousness of Thanksgiving! That does it, he's not invited back.

Root & Route

Root – (n.) The portion of a plant that anchors it to its surroundings and absorbs nutrients. (v.) Cheer.
Route – (n.) Path, direction.
Why do carrot farmers get lost in beet fields? Because they can't find their root.
...Meh, that joke sorta works.

Close & Clothes

I suppose, technically, these two words aren't supposed to be pronounced the same. But where I come from, they most certainly are.

Currant & Current

With an A – a type of berry.
With an E – (n) a flow of water or electricity. (adj.) belonging to the present time.

Soar & Sore

As in, "Can a bird soar if its wings are sore?"

Flocks & Phlox

Birds travel in flocks. Bees travel in phlox.

Hall & Haul

Gait & Gate

Gait – a style or manner of walking.
Gate – an opening or doorway in a fence.

Coarse & Course

I told you last week's map would show up again...

Cite, Sight, Site

Getting tired of seeing that book yet? :) Just wait till I start reusing the map!