A proper mess and galley. Yes, you have the lounge, but there should be a very basic mess for the crew to eat at.
Already planned.

Ammunition storage. The Fenris originally came with a missile launcher, so their should be a place to store that.
I'd thought of this back at the outset but had since forgotten about it - thanks!
A brig, every ship has a brig somewhere. Also a security office and various weapon lockers.
Ah, hadn't thought of that yet!
A laundry.
Also hadn't thought of that... not sure how we'd implement it though... dispensers maybe?
Crew quarters (bunkbeds, of course).
Yup, those will be the secondary armor layer between the outer hull and the vitals. They'll go in last, to fill up any and all unused space.
I know I saw the reactor, but where are the subspace coils? They're supposed to be big, so they should be somewhere in the hull (forward section perhaps?).
Ahh, perfect! That's what those side red things can be, Hades! We'll have to carve out room for the internals - I'll try to do that tonight.
Auxiliary control, in case the CiC gets taken out.
Maybe, but did you see where the CIC is located? If
that gets taken out, the entire ship will have been carved up already and out of commission. Still, I guess an internal problem could knock the CIC out, so this makes sense.

Cargo stores.
Ooh, good one... does it make sense for the existing airlocks to be used for cargo conveyance, or should we be looking on the texture for markings to indicate secondary dock points?
When I get some time, I'll try to help, but I have other projects first.
Make sure to ask for creative mode from qaz if you get to that point... I don't think he'll hand it out willy-nilly, but for work on the Fenris he's been willing.
Machine shop
Good one.

Damage control stations (lockers that contain equipment for patching hull breaches and temporarily shoring up the ship structure)
First aid points
These are great ideas, they're just the thing we needed to break up the monotony of those infernally-long corridors - little alcoves scattered about.
Captain's quarters
I
think Kyad may have already done those - enter thru the airlock, head forward, and turn towards the middle at the end of the corridor - there's some quarters in that cross-section.
Sensor control/equipment/maintenance room under the radar dish
Also something I had planned a while back and since forgotten - thanks.

food/general waste disposal/re processor
bathroom/toilets
Air Handling Compartment/temperature control
We'll probably lump all that (besides the bathrooms of course...) into one large "Environmental Control" room somewhere.

Bathrooms will be part of each officer's quarters, centrally located near crew quarters, and strategically located near crowd-gathering facilities (mess hall/lounge, bridge, engineering, etc).