If your a new rider, the Ninja 300 is a great bike strait from the dealer. Mods should be something that YOU think the bike is lacking after riding it, or something that you like to personalize it to YOUR taste.
A slip-on (exhaust muffler) is probably the most common modification that people make, it makes your bike sound way better, and you get a few extra horse power and they look cool on your bike.
Also a fender eliminator is a part that takes off the huge ugly rear license plate holder, tail light and rear blinkers, and puts these things in a much smaller and more attractive unit that makes the rear end of the bike look much better. (I still don't know why manufactures make them so ugly)
Frame sliders are another one of the most common additions and are one of the most useful if you ever drop your bike or crash it. A bolt on piece that most sport bikes have.
Those are probably the 3 most common mods for ANY sport bike. I will say that I think a Power Commander is probably a waste of money unless your getting a full exhaust system and plan on doing some seriously aggressive riding, and even then, it's something that you would add to your bike after you've gotten to the point where you can ride the bike to it's limits and want more performance.
My personal recommendation for a first "mod" is a new set of tires. The stock tires are not very good, and if you think about it, great tires can be the difference between a great ride and a crash. I know it's not a very "cool mod" but the tires are your connection between your bike and the road, so it's kind of important, especially if you plan on doing any "spirited" riding. And yes, I just put on a set of Pirelli Diablo Rosso II's, and they make a huge difference in how my bike rides.
Be safe and have fun