Heres my humble toughts
First rule, you need more space then you planned. Trust me...
Second rule, keep most important tools at electronics bench: power supply you use, oscilloscope, multimeter, etc... In fact you electronics desk should have its own shelf for these most likely.
Third rule: Tools travel... Other tools should have their right place as well, otherwise they will travel to your desk...
Have separate computer desk close by electronics desk, you will want to look those datasheets often... Even better if you can manage flat monitor, small keyboard and mouse on electronics desk somehow. Computer itself should not be on desk, it takes already precious space.
If money allows, get one of those good quality anti-static mats thats cut and heat proof..
Small components, have separate shelving for organizing them.
Light, you need more of it then you think now. Consider adding more. If electronics desk has shelf for bigger items, under that is good place for some led strips for extra light.
Good, easily view-able clock, So you remember to get some sleep when its hitting 4 AM and your doing super interesting project...
One more thing, power strips, you need them, you need one or two more of them then you think... My desk has places for 7 power hungry items and im running out and need upgrade bigger strips soon.. After adding oscilloscope i have one empty socket left...