I am going to get a standard sized rabbit. It's going to be in an exercise pen most of the time; how large should the pen be?
By an exercise pen, I assume you mean the portable style generally sold for use with dogs. I also assume that mean to use it inside, as John points out in his answer, using an exercise pen outside for a rabbit (unsupervised) is essentially a death sentence for the rabbit.
In some cases it is not practical to bunny proof all of your house, or if you need to keep the bunny separated from other animals or any number other reasons, a X-Pen (exerciser pen) is a common solution. The standard pen is made of 8 panels 2 feet long. As a square this gives a space of 4 x 4 feet, which is too small for long term, but ok if the bun gets out to have run of the house for at least an hour everyday (two hours twice a day is better). One X-pen used in conjunction with a wall or corner will give you a much larger space, optimally a space of 8 X 8 feet can be used for long term housing. If the bunny is NOT able to run and jump in the space it is NOT big enough. See related question How much space does a rabbit need to live comfortably?
As for height, in most cases a 2 foot high X-pen is tall enough, but I have known rabbits to jump over a 4 foot high pen. Leave at least a couple feet of space between the x-pen and anything about the same height (like furniture) on either side of the pen. Though many people I know, feel more comfortable using a 3 foot high pen.
Why is 2 feet tall enough? A rabbit will stretch up and look at something like a couch and see "Hey that looks comfy" and then jump up on it, but if there is not a good place to land on a place that can not see, they tend not to jump there. If there is nothing to land on at the top, they don't go. EXCEPT for the rare bunny that been trained to jump over something, where they can see a good landing place on the other side.
A rabbit will see an X-pen as an obstacle and they will pull and tug, and move it around trying to get past it. If using a X-pen with a wall fasten it to the wall, we use small round eye hooks fastened to the wall and clip the pen to the hooks.
I am a little unsure of what you mean by a standard sized rabbit. I have a dwarf rabbit, but the excercise pen that I have is meant for small dogs. I believe that if she wanted to she could easily jump over it, but she chooses not to because she has so much free room . I am not exactly sure of the size. However, there are also some excercise pens that are really small, and I don't believe it is fair to leave an animal in them. If you plan on keeping your rabbit in there most of the time, I would reccommend one that is for dogs, because they will give your rabbit plenty of free roaming space.
Rabbits vary in size, so actual breed would probably be helpful. However, I think you should consider a few factors:
Rabbits can jump, some of them as much as a meter. So any fencing should consider this as a factor.
You didn't say if this pen is inside or outside, but if I assume outside, consider that rabbits can dig. In that event, you want the pen fence to go into the ground a ways.
Still assuming outside, bear in mind that there are rabbit predators that strike from the air. If you cannot entirely cover the pen, you should shelter it and should have a place for the rabbit to escape to.
Rabbits need some running space and are known for engaging in bursts of manic running known as the Bunny 500. You want to give them some decent space to pull this off, so I would be looking at least 10 x 10 foot, but that's hard to find pre-built.
If the bun is intended to be indoors, then consider not penning them. Do some room proofing, and provide a litterbox for them (they can be litter trained easily). You just need to take some precautions with chewable things like wires and cords. Doing this will allow much more interaction with a very social animal and your relationship will be more rewarding as a result.