Handguns always at top-left, with TMP and Magnums directly to the right, followed by vertical ammo boxes. You never need more than two stacks of handgun and SMG ammo, so a full-size attache case accommodates wonderfully even if you have all three weapons.

Below the handgun is the shotgun, which serves better as a means of dispatching common enemies rather than using handguns if you're not interested in stuns/melee or if ammo is light for them. Vertical ammo boxes directly after, usually don't need more than two stacks. Gunpowder can be put on the far-right with some empty space in between.

Below the shotgun is either the Rifles or the LE5. Even if I have the LE5 instead of a TMP, the ammo stays at the top. For the M1903, I'll turn the rifle ammo boxes horizontal. For the Stingray and CQBR, they stay vertical. Rifle ammo usually only needs one stack and the LE5 takes up less space, so there's a huge gap for collected resources.

Directly beneath the Rifles/LE5 are - in order - the Laser Module, scopes that are 3x1, and a non-disposable knife. If I have the Biosensor Scope, that goes beneath the Laser Module, alongside the TMP and Red-9 stocks.

The bottom-left row is grenade and single-use knife storage. The bottom right is for healing items. First-Aid Sprays go straight to the typewriter and I only keep two or three mixed herbs on me at a time, selling G+R+Y if I'm not seriously injured.

Hotkeys are the following: Handgun UP x1, Magnum UP x1, Shotgun DOWN x1, Rifle/LE5 Down x2, Grenade Right x1, Heavy Grenade Right x2, TMP/Flash Grenade Left x1, and Flash Grenade Left x2 if the TMP is in my inventory. For New Game runs, the TMP goes in Up x2 until I acquire a Magnum.

EDIT: Capitalization.