Assuming "upgrade" means "has no downsides and additional non-cosmetic upsides", the current list would be this: Third Degree (
same as Fire Axe, but also damages everything else connected by medigun beams)
Hotrod (same as other hats, but due to a bug, if a Spy's disguise is wearing one and he's holding a Sapper, it'll flip over his face and expose him to attentive players)
There are not currently any other pure upgrades in the game -
any weapons that seem so are either purely cosmetic differences (Golden Wrench's Australiumization effect), replace a weapon with a support item of uncomparably different functionality (Sandvich, Gunboats), or have an upside that significantly outclasses the downside (Amputator having a healing taunt is much more important than the 20% damage reduction, which while probably technically an "upgrade" I don't think is the purpose of this question).
gaming.stackexchange.com/users/12939/Toomai
Nearly all weapons that are not "default" either have a penalty attached to them, or change drastically the nature of that weapon slot.
So items that are nothing but an 'upgrade' are very rare.
Here are, as far as I know, the items that exclusively add to a "stock" item's ability, with no downside or change in functionality.
Fire Axe
>
Third Degree - Adds "shared damage" between targets attached by medic beam.
Bonesaw >
Amputator - Adds healing taunt that heals multiple team members at once.
Fists >
Holiday Punch - Causes target to laugh when struck from the back (stunning effect)
Bat > Fish? - Special Kill Tracking (You might consider this an upgrade, or you might consider it a downgrade that reveals your location)
Note: Amputator and Holiday Punch both have downsides.
The Amputator does -20% damage, and the Holiday Punch does no crit damage.
gaming.stackexchange.com/users/55285/Zibbobz
There are only 2 direct upgrades in the game.
The Third Degree: With no downsides, the only upside is that this weapon hits enemies that are connected through a Medi-Beam.
The Solem Vow: With no downsides, the only upside is that this weapon shows you the HP of enemies that you are aiming at.
Weapons such as Ali Babas Wee Booties, Targe n'
Charge, Kritzkrieg, RazorBack, ect, ect are side grades.
Even though they have no downsides (stat wise), they do take up a slot.
The Booties take place of your Grenade Launcher, and the shields take up your sticky launcher.
Same with the Sniper Backpacks, Soldier Boots, and Heavy Food.
The Kritzkrieg (with no down stats) is a side grade as well.
It turns your invulnerability into insta crits.
The equalizer/escape plan are great melee weapons, but they prevent being healed (and the escape plan makes it so you take Mini-Crits while out), so they are not upgrades.
I hope this cleared up the above answers.
gaming.stackexchange.com/users/9608/Shadow Z.
Have a look on the official wiki http://wiki.teamfortress.com/
Most of weapons are "upgraded" in TF2, we can't list all of them here.
If you're looking only for "full bonus weapons" (which is not really true), here's your list : Gunboats Mantreads Equalizer
Ali Baba's Wee Booties Bootlegger Chargin' Targe Splendid Screen Dalokohs's Bar
Fishcake Apoco's Fists Pomson 6000 Golden Wrench (the only one truly upgraded) Krietzkrieg Amputator Solemn Vow Razorback Darwin's Danger Shield Cloak & Dagger Saxxy
gaming.stackexchange.com/users/24962/zessx
Almost all of the weapons you can drop or craft are upgrades from the default weapons.
The dev team has always tried to do a great job in balancing the power of your enemy-killers.
That's why most of them have a "malus": you have to weight, considering your playstyle, the great things that your weapons do and consider if those outshine the bad part.
The weapons that don't have a red text usually are made that way because they have a way of functioning that completely substitute the normal behaviour of the weapon for that slot.
Take for example the "shoes" for the soldier or the demo (Mantreads, Gunboats, Bootlegger...): to use those you have to completely give up the secondry weapon slot, getting a passive bonus instead.
The same applies for the shields for the demo or the sniper.
Medic's alternative healing guns completely substitute the Overcharge mechanics.
Amputator's "bonus" requires a taunt, that effectively makes you lose control of your character while executing it.
Third degree's bonus?
It's almost always a suicide getting with a Pyro in melee range of someone getting healed by a Medic.
You have a great freedom of choice and the official wiki can be a good place to get a good idea of what can be a good upgrade.
gaming.stackexchange.com/users/23609/Kappei
I've been looking for weapons that are upgrades from the default weapons in TF2.  Ex. Third Degree.  It's techinically an upgrade since there  are no downsides and it hits players via Medigun beams.  Are there any other weapons like this?
Which weapons are considered "upgrades" in TF2?
gaming.stackexchange.com
<team-fortress-2>
gaming.stackexchange.com/questions/65206
gaming.stackexchange.com/users/18916/korrasaur
Weapons that are not default have a penalty attached to them. The Third Degree hits enemies that are connected through a Medi-Beam. The Solem Vow shows you the HP of enemies. It seems that most of weapons can be upgraded.
The community tries to define what default weapons might be and gives a definition regarding the upgrading.