Now, before we get into this, there are two things you should know about: IVs and EVs. IV stands for Individual Value, and is a value from 0-31 that determines the stats of a Pokémon. Each Pokémon's IVs are determined when you catch or breed it, and can't be changed. Pokémon have one IV for each stat, so one Attack IV, one Defense IV, and so on. IVs are what make each Pokémon unique, and why two Pokémon of the same nature have completely different stats. (IVs are like a Pokémon's genes; everybody's different.) IVs also determine what type attack the move Hidden Power will be.
EV stands for Effort Value. Each Pokémon starts with 0 EVs, and gets more as they battle other Pokémon. Each Pokémon is worth a certain number of EVs; for example, Ninetales is worth 1 Special Defense, and 1 Speed. A Pokémon starting with 0 EVs that defeats a Ninetales in battle by itself will end the battle with 1 Sp. Def. EV and 1 Speed EV. 4 EVs in a stat equate to one point of stat growth. Pokémon can have 510 EVs overall, with 252 per stat.
Generation VI greatly simplifed this whole process by introducing Super Training, allowing players to train for EVs more efficiently, and without having to know which Pokémon are worth what EVs, and so on and so forth. (Let me tell you, it was a pain in the ass before then.)
So, what's the best way to train a Ninetales? Full disclosure: I'm not into competitive battling, I mostly just battle against the NPCs and whatever the current gen's version of the Battle Tower is. If you're looking for competitive strategies, spend some time at Smogon. Ninetales isn't the best choice for a team, but now that it's got Drought, it's not a bad one, either.
nature & evs
It's very rare that I don't go with Modest for Ninetales (+Sp. Atk, -Atk); Ninetales doesn't need its Attack stat and you want the boost to Special Attack. However, Timid (+Spd, -Atk) can be useful if you want a particularly speedy fox. Either one is a good choice.
Your EV spread often depends on what you're looking to accomplish with Ninetales. For movesets heavy on attacks, I tend to put a solid 252 points into Special Attack; in others, I split them up into Ninetales's defenses and speed. Experiment and see what works best for you.
I used this set in my SoulSilver playthrough, to good effect. Ninetales's base Sp. Def. is high enough to take a STABbed Water-type move and survive, and EVs only ensure that. Will-o-Wisp guarantees that the other Pokémon's not getting out of this easily; Confuse Ray keeps it occupied, and while Attract is a tossup, it's nice to have. It can be swapped out for Fire Spin to trap the opponent. Flamethrower is made even more powerful by Drought in later generations.
I used this set for my X playthrough. Extrasensory is a good substitute for Psychic (which Ninetales can't learn), and Drought's sunlight helps deter Water-types. Confuse Ray and Fire Spin, again, are good to keep the other Pokémon distracted if the opponent isn't a type Ninetales can easily deal with. Energy Ball is also a great option; it can be taught via TM and Ninetales can hold out well against Water-Types with proper EVs. (252 Sp Def/252 Sp Atk/4 Spd is a good spread for this moveset.)
This set takes full advantage of Drought, keeps the sun up when it goes down, and ensures that Ninetales's Special Attack can annihilate most anything on the field. It does still have its downsides, in that Ninetales's Special Attack isn't the greatest, but it's a good set for what it has available.
Like I said above, Smogon has other options for Ninetales if you're looking to play competitively. For use ingame, though, these sets should see you well on the way to victory.