Hi Scott...
A good question, to which the answers will vary and no doubt be contentious
I come from a military flying background, where there shall be nothing "loose" in the cockpit. It eithers goes in a Velcro pocket (checklist / map) or is tied to you (pen), or has a secure stowage (pitot cover). This is to minimise things flying about during manoeuvring (aerobatics) and Loose Articles getting into the controls (which adds another discipline of ensuring everything you take into the cockpit is removed after flight, else aircraft grounded until it is located).
Clearly we cannot all be expected to adhere to this, but it is a starting point. As such, in our RV-8 (and it seems pretty unusual in this regard), stowage is a priority:
- Vans Map Box in the Panel. The cheapest real estate going in Panel terms, and I still think about the most valuable. All sorts of paperwork / tools / phones / water bottles etc. goes in here. Just clear it out from time to time...
- Right "Mid Cabin Cover": keep space below clear of wiring and fuel pipes, and fit a storage compartment with a lid that can be secured. Ours is just a fibreglass box with AL sheet lid. Takes chocks, pitot cover, fuel drain, fuses etc.. - "permanaent aircraft equipment".
- Left Mid Cabin Cover: Ensure Fuel Valve etc. as far forward as possible, and again, keep fuel piping / wiring away from under rear half. Another fibreglass box, open this time, but can use elastic straps from the screws. Takes short terms stuff e.g. water bottles, food.
- Sidewalls: material pockets for maps etc.
Effect is we can carry a fair amount of stuff, yet still be safe for aeros etc.. With regard to your post:
- Check List: Small one goes under roll bar flanges on windshield
- Fire extinguisher: Don't have one... but if you wish, they seem to go on aft of Gear Tower?
- Gloves: On hands!
- Flashlight: don't have one, but we cannot fly in the dark
- Battery pack for ANR headset: Don't have one - use helmet or headset with ANR powered from aircraft electrics
- Ipad holder: Ummm, don't have/need iPad in cockpit
- My existing flight bag What is, and goes in, a "flight bag" for GA type flying??
- Some stuff fits in the back seat's foot wells This works OK until a back seater puts their feet there. Digging your sandwiches out from under a size 10 boot tends to make lunch less appetising

In short, some discipline during building and flying can go a long to addressing this issue.
We setup a UK RV Formation School using largely current and ex-Mil instructors. The biggest issue early on was "loose articles" - especially the SBS RVs where the stuff just "dumped" in the baggage area was amazing. The "students" (owners) took a little adjustment to the concept "we don't even strap in until that area is
empty"

But the idea got there...