The classrooms at my school are designed for maximum flexibility and maximum visibility: we use chairs that are easy to move and to stack, wheeled tables that can be easily combined to make larger tables, we have lots of glass walls, and most classrooms have one wall that can be opened to turn two classrooms into one big classroom.
For most of what we do at school, this flexibility is ideal. However, projects also need some specialist spaces and some specialist equipment.
Here's my list of spaces and equipment that an ideal PBL school would have:
Specialist spaces:
Garden (designed with a few raised beds so you can have separate control and experimental groups)
Test kitchen
Recording/film studio
Some kind of lab (I'll be honest, I have no idea what a good science lab needs, other than flat surfaces that don't wobble - which I know about because they're surprisingly hard to come by at our school).
Wood shop/Maker Space (personally, I would emphasize stuff like drills and table saws over 3D printers).
Black box studio theater with basic lighting.
Specialist equipment that doesn't needs a purpose-built space:
Musical instruments
Sewing machines
Costumes
Books
Computers with publishing, design, engineering, and audio and video recording and editing software.