Buying an '07 Ninja 650R, and I was wondering what gear/tools/anything you guys would recommend for riding and upkeep.

Can't wait!

Everyone has different priorities (as well as assorted tools) so I'll give a run down in the order I'd buy. The first three BEFORE you ride.
Helmet
Gloves
Boots
Pants
MC specific tools (chain brush, cable lube tool, filter wrench, etc) as you need them, assuming you have a decent assortment of hand tools
Bungee cords or a bungee net
Tank bag/tail bag (your choice, I have both)
Swingarm stand (not essential, but very handy for chain maintenance and tire changes)
Lock for security, may be higher on the list depending on WHERE you live and where the bike is parked
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rim stripes

Motorcycle safety course!

Yes. MSF course first. You will learn a lot.

for the bike. Frame Sliders. There is a good chance you will drop the bike on its side.

For you, Full Face Helmet, Gauntlet Gloves, Jacket with CE armor, Motorcycle boots with ankle protection, Riding jeans or pants.

Wear your gear every ride. It's the ride when you don't wear your gear that you will go down.

1. GEAR GEAR GEAR!!=> Helmet, gloves, jacket, pants, boots. make sure to look for CE approved aromor in your gear. look for gear with retro reflective stuff on it. who cares if its goofy looking "CAGERS" do not pay attention and we need to give them every oppurtunity to see us. if you dont like the way the pants fit a good option is some t-pro forcefield armor Forcefield Body Armour Pro Pants | KneeDraggers and some kevlar jeans.
2. msf course. this is number 2 cause you need gear to take it.
3. chain cleaning tool and chain wax or chain lube whatever you prefer.

if your bike came with the original tool kit you can use that for quite a while. it should have the tools to do most basic things you will ever need too. i have plenty of tools and still use my toolkit because it has the for sure sizes i need rather than digging through all my stuff. the three things i listed will get you going and KEEP you riding for a while. you need to clean and lube your chain about every 400 miles so #3 is definately a necessity. my first STREET bike was a ninja 650 as well. have fun and ride safe!!