I am planning to build into Alex's closet when we move his room downstairs this summer. There is a built in closet and a built in dresser in his room... but he only really needs the dresser... so I am going to take the doors off the closet and make that his book shelf. Then I am making him a loft bed, and putting a curtian under neith it on one side with a desk on the other under the ladder. That way he has his own study space with out taking away from the play space... although your children are going to be MUCH younger... so these may not work for you. I agree with the baskets idea... it is an easy and stress free way to keep dipes, wipes and their wipe solution bottle all in one place... you can find good baskets for things like this at Target or even Goodwill.
Could you nix the twin bed in lue of another crib or toddler bed? (Some children have a hard time giving their bed up for the new baby... I know that Alex did. Be prepared.

) Perhaps change them on the floor? (I never had a changing table... I just vacuumed every day.... and at first had a really pretty changing mat that I used) A shelf with baskets with toys in it? Small shelves are very easy to build and cost next to nothing when you build them yourself. This is what I have in both mine and my childrens rooms. They are 4'X4'X8"deep... they have worked for everything from cd's and a stereo to books too tall to be on the built in shelves, to Cyans diaper stuff and all baby toys.
Good luck and congratulations on the new baby!!!!!!
Love Val