If they are vintage brushes, best to separate them into groups fit for a certain car.
Aurora tjet brushes are copper and flat on both sides.
Tough Ones/ Wild Ones are silver and flat on both sides.
Afx non-mag (like JL Tough Ones) have a notch on one side, and are domed on the other.
Afx M/T (like X-Tractions) are flat on one end and have a nipple on the other.
To avoid any problems use brushes intended for that car. If you are short, many online stores (SCJ, Jag Hobbies, Bud's HO, and others) have plenty of each.
The AFX Domed silver brushes can be used in TJETS and JLs. They work very well in my opinion however they do dirty up the commutator a lot faster. The only major down side is most racing rules do not allow them to be run. If you have lots of AFX brushes and are tring to get some TJETS up and running to cruise around your track go for it. If you are planning on racing them then don't use them.
Although the TJet/AFX brushes are all about the same size and will work to some degree in just about any chassis, it's fairly obvious which ones are intended for which chassis. The brushes with the notched bottoms work best in chassis with notched brush springs/holders. Flat brushes work best when they have to ride atop a flat topped brush spring. Flat brushes will work with notched springs/holders but they may spin in their holders which may reduce their performance a little bit. Brushes with domed tops (original AFX and JL TJet) give a little added performance by reducing the brush friction against the commutator and reducing fouling, but if they aren't sitting properly in their holders they tend to roll over a bit and wear unevenly and may even turn sideways and bring the motor to a halt. In cases where domed brushes cannot be kept properly aligned (perhaps due to overly large brush holes or malformed notched brush springs) you are usually better off using flat brushes and taking the small potential hit on performance.
Like Roger said, brushes come in different materials and the different materials provide different performance levels. Aftermarket brushes like Wizzards or Thunderbrushes are formulated with compounds that are intended to provide better performance than stock brushes. Copper compound brushes have more current carrying capacity than silver compound brushes but have more of a voltage drop. Different brush materials affect the wear on the commutator differently so a brush formulated for better performance may reduce the life of the motor. Some folks mix materials and run a silver compound brush on one side and a copper compound brush on the other. The rationale is that it's intended to give a small boost in performance while keeping comm fouling a bit lower than if using all silver compound brushes. Brush tension is a huge factor. Too little or too much is bad. Temperature and humidity also factor into brush performance. There is no magic formula for choosing brush materials or setting up brushes. There are always tradeoffs and the best approash is testing, testing, and testing.
I've found that the notched and domed brushes that come with Johnny Lightning TJet500 chassis work fairly well on TJets and original AFX cars. I prefer them over the original AFX silver compound brushes.