It looks like you have the basics covered pretty well. Until you really get to spending a lot of time on the bike, you won't know what equipment best suits your needs, so there aren't many wrong answers when it comes to brands and models. As you get more familiar with your bike and personal needs, you will find yourself getting more particular about what accessories fit your needs the best.

Before you go on a spending spree, give a quick thought to were and when you will actually be riding. If you are going to jump right into sharing the road with automobiles, blinkies, reflective tape, and hi-vis vests can never be a bad thing. However, if you are only riding in full daylight, on multi-use-paths and well marked bike lines, I don't think these items are the best place to spend your money. Spend a couple bucks on an Incredibell and use the rest of what you would have spent on visibility items to get a little nicer helmet, saddle, or shorts.

While the bike is still new, don't hesitate to take it back to the bikeshop and swap saddles if you need to. Most shops will gladly do this for you. If you find the saddle uncomfortable, you are less likely to ride the bike. Comfort is paramount to enjoying your new bike. Find a saddle that is comfortable. It's cheaper to do this while the local bike shop is willing to make the swap for you.

For the most part, a helmet is a helmet, but just buying one off the shelf because its cheap is foolish IMO. Protection wise, a $30 Bell is no different than a $300 Giro, but there is a HUGE difference in fit and comfort. You don't have to spend a lot for a good helmet, but it really is a personal item that should fit you well. Try a few different helmets on and pick the one that fits your dome the best and has a comfortable retention system. Full face jobs are for motorcycles, BMX, and hardcore downhillers.

Shorts are another personal item that should be more about fit and comfort than features. If I'm just riding a short distance, or going to the store or farmer's market, baggy shorts with pockets are fine, but if I'm riding for the sake of riding, I'm much more comfortable in tradional tight shorts with a well designed chamois. More padding is not necessarily better. Shape and placement of the chamois is what makes being in the saddle more comfortable. Bicycling shorts are tight and close fitting for a reason. Loose clothing can lead to rubbing. Rubbing leads to chaffing. Chaffing can lead to infections and extreme discomfort in very sensitive areas.

What do you need with a toolset? Do you have enough familiarity with the bike and it's parts to be comfortable making repairs and adjustments on the side of the road? Do you know how to use all of the tools you might need? This is another item I would wait on until you know what you are actually going to use, but if you must, I like the Crank Brothers M-17. It is likely to have everything that you might need while on a ride.

Definately keep a spare tube, a patch kit, and a set of tire levers in your saddle back. Familiarize yourself with changing tubes in the comfort of your living room. Last fall I helped a guy who had all the right stuff to fix a flat (on his $4000 road bike), but didn't know how to use any of it. Had someone not stopped to help him, he was a three mile hike up the MUP to the nearest intersection where his wife could pick him up with a car. If I flat, I usually just replace the tube and patch the the flat in my easy chair at home, but I carry the patch kit with me just in case. A patch kit with multiple patches will keep you riding much longer than a single spare tube. I will ride a tube with up to three patches.

If you are going to try to use it to commute, you will want a rack for the bike and a trunk bag, basket, or panniers. A lot of people get by with backpacks or messenger bags, but I find them incredibly uncomfortable to ride with. I feel unbalanced, and I get to my destination soaked in sweat. Once you figure out how to pack your junk on the bike, you will never go back to packing it on your body.

If you get a bike with an alloy seatpost, a seatpost mounted rack and trunk bag will suffice for most short distance, lite commuting. If you have a cf seatpost, you will have to put a real rack on the bike.

IMO, the easiest way to carry your U-lock is bungied to a rack. I wouldn't want it in my frame triangle, personally.

Most saddle bags are mounted to the saddle rails, but I wouldn't be too bothered to mount a lite toolkit to a cf seatpost.