There are very few weapons that are completely unusable compared to their alternatives. The razorback, crit-a-cola, the bonesaw and the shovel are the ones I'm thinking of (I'd have said gunboats, but apparently they have some use in comp getting medic picks or such, which would explain the mystifying nerf they recently suffered). The rest of them are either well-balanced or are in that awkward 'pre-buff sandvich' area where one often thinks 'gee whizz, it sure would be useful if I had a homewrecker/bonk/backburner', but their use isn't broad enough to be carrying them around just in case. Once the opportunity comes to reequip, the situation has passed. They're things one would use to solve a specific, occasional problem, but wouldn't want to carry around waiting for the problem to arise.
That said, I think a lot more of the items could use some kind of tweaking, so I'm going to go through the list of items on TF2wiki and talk about them:
Scout
FaN: I actually don't mind this, I just wish it was less widely-used. It's not as good for killing dudes as the scattergun, but I find its knockback useful for clearing objectives and blunting the attacks of close-range classes. In addition, Valve seem to have started designing maps more and more to increase the value of knockback with cliff edges and such. So I'll leave it largely as is, but maybe make the third jump a little less awkward to use; if, instead of applying 'forces' and such to the poor fellow, it just launched him backwards at a given velocity, I suspect the triple-jump would be a tough more significant than it currently is.
Bonk: Replace the bat rather than the pistol.
Crit-a-cola: Remove the downside. It's not worth losing the pistol for something that has a downside as well.
Sandman: Just get rid of the stupid sandman.
Soldier
Equalizer: Remove the additional damage, and leave it as a way of escaping at low health. It'll still be pretty darned useful. In fact, also increase the health cost of rocket jumping a little. He can't jump as much, but he can still move fast. It might also increase the value of gunboats to compensate. A rocket-jumping, fast-running soldier (with no shotgun).
Pyro
Backburner: I'm not really sure. Extra speed would be welcome, to make him actually decent at flanking. Or maybe, uh, +50hp. For balance.
Or wait, how about a smokescreen, firing a cloud of smoke that hangs around, impairing vision and causing damage comparable to afterburn to opponents in the area. It might help to get around an opponent in direct confrontation, and also provides a little area denial. It'd probably be pretty useful, and make up for the disappointing absence of a secondary fire.
Homewrecker: I'm, uh, wait a second.
Fire axe: Give this a speed bonus and it can be friends with the backburner, which doesn't need the axtinguisher if it actually gets the chance to flank anyway (or, whatever, give everything else a speed reduction and increase the basic speed of the class, that's fine too).
Homewrecker: Bring it up to normal damage against players. Instead of having an ass downside, it's got an upside that's sometimes useful. Still not as good as the axtinguisher, though.
Demo
Scottish Resistance: Just make it a little less awkward to set off the bombs. Looking in their very general direction ought to be enough.
Beef
Natascha: Reduce the movement speed while spinning to pre-buff levels, so the beef can't chase people around corners so effectively. And cancel the slowdown on rocket jumping opponents.
Dalokohs bar: Give it a medic-style passive health regen, and increase the amount healed to a damaged beef (maybe 120 like the pre-buff sandvich, which was weak on its own but would probably be useful with this additional combination of abilities).
Engineer
Gunslinger: An extra 25hp for the sentry would allow it to get a few extra hits in when it's been spotted, and allow it to finish constructing under pressure (gunslinger engies are currently too weak on the back foot to pass as a decent attacking class). And make the teleporters cost 100, because that extra 25 metal is a real killer and discourages building something an engy really should be encouraged to build.
Medic
Bonesaw: The bonesaw isn't really bad, it just doesn't compare well to the ubersaw. It's the same situation as the syringe gun/blutsauger used to have, and that was resolved pretty well; now both weapons are useful if the medic wants to make them useful. So we could give the bonesaw a slightly higher rate of uber generation (nothing drastic, maybe around 10% or so), or reduce the ubersaw to make that the case. In the same way as that the blutsauger is massively better when the medic is actively firing needles and worse at all other times, the ubersaw would be a huge upgrade for medics who get the chance to hit an opponent with the ubersaw, and a genuine loss for those who weren't going to actively use it.
Sniper
Huntsman: I'd give the huntsman an extra 25hp. It's still fragile, but a standard-speed, 125hp player who has to slow down before he shoots is not a credible threat in the kind of situations where the huntsman should be optimal.
Razorback: Increase scoped movement speed. That would make it actually worth considering for both rifle and huntsman snipers (especially rifle snipers who stay way at the back, where neither jarate nor the smg are greatly useful).
Tribalman's shiv: Perhaps the actual damage element of bleed effects ought to be lessened. Its main function is to reveal spies, and it's better that way. If the two melee weapons are designed to offer comparable damage, it's not really an interesting choice between the two (although even if they were, the kukri would be better for real melee combat). It goes for the southern hospitality was well, but I think it shouldn't be taken for the purpose of dealing damage. I see it as an anti-spy item like jarate, rather than a genuine fighting weapon. It's also a useful effect for snipers who want to use something other than jarate in their secondary slot.
SMG: I suppose it could use a few more shots in the clip. He's not meant for close combat, but the SNG currently leaves him so defenceless that there's not much reason to take it. I'm happy with the damage being low, but reloading leaves him too open to be as frequent as it is.
Spy
Ambassador: Ugh. I don't like the mechanics for this at all. When it was described in the update reveal, I wasn't expecting something weaker than the revolver. Currently, unless you get a pinpoint headshot, with the first shot, it's useless. I'd have a reduced clip size (2 or 3), much higher power, and a little more accuracy than the revolver. Leave the headshots, or ditch them, I don't care. I'd ditch them. But if it could do around 80 damage per slug, with a slow rate of fire and decent accuracy, it would be a neat choice. It wouldn't open up any new playstyle (it would play just like the revolver, although even more discouraging to direct combat), but it would be good as an option.