I like everything clean and organized. However, for me it depends on a few variable factors.
1) First it depends on what level of construction I am currently in (right now, constant). If I'm doing a lot of cutting of lumber that will take a few days I'll wait until I complete an area before I clean it up. I like to get from point 'A' (the start) to point 'B' (completion) as fast as I can, so unless dirt and debris are in my way I wait until I'm done to clean it up.
2) Clutter is directly proportionate to the storage space I have vs. the growing train inventory. Right now during my redesign I'm relocating items that I won't be using until much later (scenery, buildings, etc.) to a spare bedroom as I lose storage space under the layout where I am making changes, then move the displaced trains into the vacated storage areas.
3) My wife is a self proclaimed 'pack rat'. Not anything near a 'hoarder' but she has some personal possessions stored under the layout. I don't mind as it's a small price to pay for having the whole basement…errr, Train Room 'to myself'. I don't want to damage anything during deconstruction. Negotiations are pending.
Now, once heavy construction is completed (yes it WILL happen) then touch up painting, room decor and thorough cleaning will make it a comfy and fun place to run trains and entertain. Then I can keep the area and layout clean as I go from there.
But remember what they say, a clean desk is a sign of a sick mind!! 
