Question: You've just written a pile of code to deliver some important feature under pressure. You've cut a few corners, you've mashed some code into some over-bloated classes with names like SerialIndirectionShutoffManager..

You tell your boss you're going to need a week to clean this stuff up.

"Clean what up?"

"My code - its a pigsty!"

"You mean there's some more bug fixing?"

"Not really, its more like.."

"You're gonna make it run faster?"

"Perhaps, buts thats not.."

"Then you should have written it properly when you had the chance. Now I'm glad you're here, yeah, I'm gonna have to go ahead and ask you to come in this weekend.. "

I've read Matin Fowler's book, but I'm not sure I agree with his advice on this matter:

* Encourage regular code reviews, so refactoring work is encouraged as a natural part of the development process.
* Just don't tell, you're the developer and its part of your duty.

Both these methods squirm out of the need to communicate with your manager.

What do you tell your boss?

Answer: 
It's important to include refactoring time in your original estimates. Going to your boss after you've delivered the product and then telling him that you're not actually done is lying about being done. You didn't actually make the deliverable deadline. It's like a surgeon doing surgery and then not making sure he put everything back the way it was supposed to be.

It is important to include all the parts of development (e.g. refactoring, usability research, testing, QA, revisions) in your original schedules. Ultimately this isn't so much a management problem as a programmer problem.

If, however, you've inherited a mess then you will have to explain to the boss that the last set of programmers in a rush to get the project out the door cut corners and that it's been limping along. You can band-aid the problem for awhile (as they likely did), but each band-aid just delays the problem and ultimately makes the problem that much more expensive to fix.

Be honest with your boss and understand that a project isn't done until it's done.
If your boss doesn't understand the need to refactor or clean up code, then you have to wonder if he has enough engineering knowledge to be an engineering manager.