Bring your tomato sauce to a boil and slightly reduce the heat, allowing it to simmer uncovered to the desired consistency. Stir the sauce often to prevent burning. This will encourage the evaporation of extra water, thickening the sauce. This method does not change the taste of the sauce, but can take more time, depending on how much water you want to evaporate.
Use equal parts water and cornstarch, mix, then add it to the sauce. Only pour in a small amount at first. Cornstarch is a powerful thickening agent, so you might need less than a teaspoon for a large pot of spaghetti sauce.
After making the roux and adding bit by bit to the spaghetti sauce, you should cook the sauce for at least 30 minutes longer or you will be able to taste the grainy flour texture. You can also cook the roux before adding to the spaghetti, thus removing the mealy flour texture. Even with the additional cooking, the roux can change the flavor of your sauce, albeit subtly.
Cheeses such as Parmesan and Romano have a higher salt taste, so keep that in mind when adding salt to your sauce.
Traditional Italian cooks have been known to add shredded carrots to sauce, but it must be allowed to cook until the carrots are soft and mushy. This also helps reduce the acidity of the sauce. You can puree and sauté onions and peppers to thicken the sauce, but this will change the flavor. Try also shredding up various mushrooms into small pieces and adding them for extra thickness and a delicious umami flavor. Finely shredded eggplant also works like a charm! Be sure to remove the tough outer skin before shredding.