Good Diagonal Cutters
You'll get some really cheap diagonal cutters with your 3D printer, and you'll see some really cheap ones available online. But, once you find some good ones, you'll never go back to the cheap ones. These cutters are tough and stand up to moderate abuse. Plus, they cut flush, so you'll get a much smoother surface. I use them for cleaning up all kinds of prints.
Xecelite 4" Slim Line Tapered Head Cutter
Surgeon's Scalpels
Surgeons Scalpels are my secret weapon for cleaning up 3D prints. The blades are very sharp, easy to change out, and super cheap at only 8 cents per blade. Plus, they come with a free handle. 
#10 Scalpel Blades <-- These work incredibly well on TPU for removing support material
#11 Scalpel Blades <-- If you are only going to get one set of blades, get these. 
#20 Scalpel Blades <-- Like #10, but with a much bigger blade​
Deburring Tool
If you have your extruder leveled just a little too close to the print bed (sometimes required on large prints to insure adhesion), then this little deburring tool is a lifesaver for removing the little brim that forms. Just slide it along the edge of the brim, and the round point follows the model, easily removing the brim.
Deburring Tool with 10 Extra Blades
Hot Air Station
Some materials (like NinjaFlex or Wood) will leave strings behind, no matter how well tuned your printer is. This hot air station will make quick work of the little wisps that may be left behind. Just set it to 200C, turn the air to about 50%, and go. Be careful with PLA because you can warp it if you add too much heat.
Hot Air Station
Tweezers
Yes, you can get cheaper tweezers, but you'll never be happy with them. These are the economy version of a high-end name brand, and they are head and shoulders above the cheaper tweezers you can find. You won't regret this purchase. They grab better, tips don't bend as easily, and they stand up to a little heat. Just don't drop them on a hard surface!
Tweezer Set
Hex Screwdriver Set
It's almost as if these were designed for use by people with 3D printers. These are the four most common screw sizes on 3D printers. They are tough and hold up to abuse. You can also loosen up the set screw and shorten the bit length if needed. I've even taken out the bit and chucked it up in my drill at times, although I can't really recommend doing that.
Hex Screwdriver Set
Powered Precision Screwdriver
Like it or not, at some point you'll have to work on your printer. Yes, the provided allen wrenches will do the job, but you'll quickly tire of them. This little AAA powered screwdriver is perfect for the job. It's a little underpowered for loosening or the final tightening, but it makes quick work of the screws once they are loose.
Powered Precision Screwdriver
Wiha System 4 Bit set
Cry once when buying these. They will outlast all of the other cheap bits and keep going when you need them. 
Wiha System 4 Bit Set
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