Many amateurs or hobbyists have faced this dilemma in their own personal (and professional) work spaces for centuries nows. Two groups I know a little about are wood workers and machinists, who have written dozens of books and articles about this subject, in both the general and specific case.
0. Safety equipment: dust masks, goggles, safety glasses (with side protection), gloves (nitrile, latax, neoprene), hearing protection (ear muffs, ear plugs), and as needed!
1. Tools
2. Storage / management of those tools
3. Hard copy (dead-tree) documentation, it is being rapidly moved online thanks to cheap and compact computers and laptops, but much older reference material is still in old-school paper form (which can be handy) (example references to collect: ARRL Handbook, Art of Electronics, Machinery's Handbook, Woodworking Basics, Understanding Wood, Wiring Simplified)
4. Commonly used materials (lumber, hoses, holes clamps, fabric, sheet metal, dowels, nuts & bolts, wood and metal screws, etc.)
5. Parts (in anti-static containers for any static sensitive parts like CMOS ICs)
6. Labelling tools
7. Log / Lab notebooks . These should be paper-based, though can be complimented with online documents, a honest to goodness hard copy lab book is essential.
8. Chemicals
9. Large, easy to read clock
10. Test equipment: rulers, tape measures, calipers, digital multi-meter
11. Plenty of AC mains circuits and outlets. Preferably with a separate circuit for lighting versus wall outlets. - Avoid extended use of extension cables, and excessive use of power bars.
And time.