The only one I keep is the one for my flash, but it's in the compartment with the tripod foot of the 70-200 f/2.8L IS up against it and the pouch for that also holds a cold shoe foot stand.
I have two bags though and I'm thinking on buying two more and a case for my monolights. I definitely need another for light stands and I should have a new camera here this month. I'm probably buying another lens as well. I have my main bag, which holds a metric ton of crap and a secondary for extra flashes, cables, cords, and pocket wizards. I'm going to need the last bag for my backup body. It'll probably go in a corner though.
So if you need more space after the fact of removing pouches and such, just buy a bigger one and keep the current as a filler for overflow equipment. Also, if you have a bag with the velcro dividers, try rearrange them. I did that in my Crumpler 7MDH shoulder bag and could fit even more crap in there.