Natures will increase the affected stat by 10% during growth, and decrease the other affected stat by 10% during growth. It makes definitely a notable difference, if not a huge one. Just imagine a Pokemon with an Sp. Atk base stat of 150, such as Dialga. Hypothetically, at level 50 with a neutral Nature and full EVs/IVs, its Sp. Atk would sit at around 244 (150 + 31 IVs + 252 EVs/4 EVs per stat raise). However, with a Modest Nature (+Sp. A, -Atk) for example, it would be at around 259 (150*1.1 + 31 IVs + 252 EVs/4 EVs per stat raise). Compare 244 to 259 - a difference of 15 only, but that could be the difference between a win and a loss.
Now, my calculations may not be correct, or the method of calculations may not be correct, but the general point is that Natures are an important part of batting, even if the difference is minimal. Always try to get good Natures on your Pokemon if you're serious about battling - as I said before, it could mean the difference between a win and a loss.