So i bought a canoe...

chrism-
I wouldn't worry about rod holders at first. I've gone back and forth on the idea myself. I think they'd be both handy and a hassle at the same time. I may try mounting some at some point. Having multiple flyrods in the boat with two people can get interesting. They always seem to be in the way.
The boat you saw in the Kish report was actually my dad's. I'll see if I can find a pic of my current set up somewhere.
The first thing I did was put foam on the thwarts. I did this to quiet down when I put a paddle or rod across them. Mine also has a built in portage bar so the foam makes that a little more comfortable when carrying it on my shoulders. The foam is also nice to stick flies in to dry or to have a few lined up so you're not always digging through boxes. The foam is just pipe insulation from Home Depot zip tied on.
I also put a couple foam patches up on top of the front for the guy up front to put flies in.
If you get the right life jackets you can zip them around the seats (if you don't have a middle seat support bar) and use them as seat cushions. Mine also have pockets I'm able to put phone, keys, whiskey etc in.
The cup holders are a good idea. I got $0.99 ones at a hardware store that just hang on the side. A nice option to keep from spilling your beer. Which I've done many times.
As for an anchor- avoid the little 3lb "kayak/ canoe anchor kit" things. They're worthless. 3lb isn't enough to hold your boat from drifting in just a slight wind or current. I'd go about 7lb at least. I have a 10 lb mushroom I use. I have a Nite Ize Figure 9 Carabiner I have tied to the thwart in front of me to secure the rope. Just be super careful with anchors in rivers. They can get really dangerous really fast.
The other important thing is a couple tied off ropes in back and/or front. Helps make it easier when putting in/ taking out, tieing off to the bank when pulling over to piss, etc.
These are just some of the things that work for me. You'll definitely know more of what you want once you get it out a couple times. Over the winter you'll dream up big plans of things to do with it for next year too! Ha. I know I did. But mostly just get there and enjoy it!

Wow guys. Overwhemling amount of info. Thanks so much!

uadave - I have not canoed in a very long time, although i have conoed many times in the past. Owning one is a totally new thing for me. I also have never really fished from a canoe so that will be a whole new experience.

chrism- don't get overwhelmed. Just get out and fish it. All you need to enjoy it is a couple paddles and life jackets. Nice and simple. Everything thing else will come as you find things that work for you. I'm just letting you know the system I use. And it didn't all happen at once.
It takes a little getting used to casting while sitting down but you'll get the hang of it. Like JustinCarf said you can definitely stand up in them too. Just gotta get your sea legs working for you. We stand in mine all the time. Two people standing gets a little dicey but one is no problem.

Also, something more to think about. If you had a rod holder and you're using your fly rod, the excess line could just get all tangled up with the holder, and mess up your cast constantly. Check out a post @bfa made about his striping basket.