Is connecting your aurdino and motors that it'll drive (through a motor driver of course) to the same battery bad for the aurdino?
I mean those are small DC brushed motors, will the noise/fluctuatuons they generate harm the aurdino in the long run?

They can create problems;
and might, might damage the microcontroler if you dont have the proper filtering.

If you have the voltage regulator before the microcontroler and a shit ton of caps everywhere then you are going to be safe.

The biggest danger is when you connect motors directly to the micro's powerline. So dont do it. (i mean between the voltage regulator and the micro, thats bad)

do you have an oscilloscope available ? because if so, you can always just check how much your motors influence your battery's output, and then refer to data sheets to know whether or not that'll burn your Arduino. But with a decent voltage regulator, and as long as your battery is beefy enough, you should be okay.
Still, when in doubt, I'd rather use an independent battery for the low power boards.

@CptFox No, don't have an oscilloscope yet. So I'll just use a different battery for the board and motors.

@N0-Flux-Given How high voltage are we talking about?

@N0-Flux-Given If you're running 5V, or perhaps even 9V, a large capacitor on the ground rail of your motor should do a lot.

@ScriptCoded I haven't decided the battery voltage yet, mostly I'll use close to 6V for the aurdino, depending on the battery.
Edit: Ah. And I'll just use a similar different battery for the motors.

@N0-Flux-Given sounds good

Well, an idea.
You must ofcourse separate the connections outside the arduino (two sets of wires)
Place a diode in the wires that go to the motors because when motors stop they can return energy back.
If using lipos buy a controller (they are cheap from China)
.
Btw yesterday due to a short circuit I placed 12v in a nano plus the 5v from the USB and both Nanos and motor driver (L293D) are fine. Arduinos even the Chinese ones have protection for such cases, most likely if the motors pull to much energy the arduino will just not work but won't be damaged.

If your worrying for damaging the arduinos do like me, have like 15 different ones, 8 are unos... So I don't care anyone If I burn out one. That frees me to do crazy shit I would never do with the price of the original arduino

You can also separate the power from Arduino and motor with a ULN2003A or something like that. You can use the same battery or different power supply to a motor and Arduino (let's say you have 6, 12v motors, you use the ULN2003A to separate the power to the motors from the power to Arduino. But always connect all the grounds (-).

@GyroGearloose Thanks for the info, but I think I should keep the electronics simple and just add another battery, I'm trying to make a Bluetooth controlled rocket launcher, will post here when I have enough progress to show.

@N0-Flux-Given That's a nice one, My next project is a BT controled Rc car