These aren't all great ideas, but how about...
Spy
1. A spy knife that increases run speed, but disables the revolver.
2. A revolver with reduced clip size (possibly even as low as single shot per reload), but lets you lay a small trap that cloaks or activates after a couple of seconds. Maybe the trap deals damage when it's triggered, or stuns. It can be destroyed if it's attacked, or seen if the cloak wears off. It has a recharge time so it can't be spammed.
Sniper
1. Rifle that doesn't headshot, but disables/reduces cloak charge, and interrupts/reduces uber charges.
Engineer
1. A new primary weapon to complete the battle engie set. Shotgun that replaces your normal dispenser with a pocket dispenser. Heals nearby allies a little (lvl 1 dispenser amount?), but doesn't produce ammo. However, it lets you store extra ammo drops and dispenses them automatically.
Pyro
1. Napalm sprayer. Has drastically reduced/no direct damage, but hugely increased afterburn duration and damage. Possibly harder to remove the afterburn effect. Allow it to stick to the ground and walls for a while, and catch enemies on fire as they run through it. Alt-fire creates a longer range spray at the cost of extra ammo. Spray burns so hot, it incinerates projectiles. This weapon is intended to remove some of the pyro's vulnerability by reducing the time it has to spend in such close range, reducing the need to get so close all the time, allows it to suppress movement through an area, and let's it spend a longer time away from support and pickups, while trading off it's up-front damage.
2. Acid sprayer. Less/no afterburn, but penetrates resistance to fire and afterburn effects. Alt-fire leaves a cloud of acid that persists for a couple of seconds. It destroys projectiles and damage anything that runs through it. Maybe does more damage to buildings? Obviously, this would be part of a super awesome cosmetic set with an acid hazmat suit.
Demoman
1. Armor with similar stats to the Heavy's armor from my above post. Makes pure Demoknight more viable.
2. Grenade launcher that doesn't need to reload, but you can only carry 8 ammo at once.