Hello!
It all depends on what you want. If you want to break somebody's nose

then I guess Muai Thai would be great and you should avoid Aikido, for example. Also, do you want to train because you like martial arts in general, as an activity, or you just want to learn a few tricks...
pelicanAndrew wrote:I'm planning on taking some classes over this up and coming summer
The thing you should consider is that one summer is not enough. No matter how technically complex a MA is, you
have to train constantly in order to stay in shape and not to forget what you have learnt. Like riding a bycicle: you never actually forget how to ride a bike, but in order to ride it well you need a lot of practice. A lot! If somebody promises that you will learn something quckly (in a few months) turn around and never come back --- they just want to take your money plus you'll end up in a hospital if you try to use that "knowledge" in any serious situation.
pelicanAndrew wrote:I'm a big dude although i hope to drop some weight by summer. I have no injuries that can hold me back but i need to start doing some endurance conditioning if i'm gonna last in a fight.
If you're going to do Judo more weight is better, so try to get down on fat and build muscles instead. Don't worry about endurance, you'll build it naturally through your MA training.
Now...
1. Muai Thai --- I'm no expert, but I like it. High possibility of injury so keep that in mind, after all if you get hurt in training how are you going to defend yourself when you really have to.
2. Ninjutsu --- Great, but there are a lot of self-proclaimed idiots who claim to teach Ninjutsu. Look for Bujinkan (
http://bujinkan.com ) or Genbukan (
http://genbukan.org )! These are ONLY TWO legitimate schools of Ninjutsu in the world, everything else is Bullshido(TM). You will have to train for many hard years before you become good.
3. Jujutsu --- As there were dozens of styles practiced in Japan, and no central authority for most of them, you should be careful where you train. If you find a legitimate school, you'll learn some amazing stuff (one legitimate school I know of is Daito-ryu Aikijujutsu:
http://daito-ryu.org, but there are many more). Again, takes many, many years of training.
4. Judo --- A pacified and "sportified" version of mainstream Jujutsu. Can be quite effective in a real fight but I'm not sure how it performs when you have multiple oponents. The thing with Judo is, I have still to meet a serious practitioner (black belt, been in competitions) who doesn't have a relatively serious injury. Fscked up knees, hips, shoulders... Often to the point where they are unable to train normaly any more, and limit themselves to teaching only.
5. Aikido --- Oh, the perfection...

Yes, I train Aikido.

If you don't plan to practice for a loooong time and regulary, don't do it. You see, Aikido is perfect: it is designed for taking multiple oponents, while not harming them (well, at least not in any serious way) and it is, in theory, unbeatable. But in order to achieve that you need at least 10-15 years of serious training. Otherwise, if you get a good teacher and you're good at it, after 2-3 years you'll be able to defend yourself really good but will have to fall back to dirty tricks and "short" agressive versions of techniques (at which point it is more like Jujustsu) and real use of strikes (that is why you need a good teacher, to show you where in a certain technique you have a hidden posibility of a strike), but that will result in injuring the attacker(s), and that is not the point of Aikido, is it.

If, on the other hand, you don't have a good teacher and you're not good at it, you'll just end up in a hospital.
Any style will do, it is much more important to get a good instructor who is willing to give you the real knowledge. If you decide to take Aikido, one important advice: don't frown upon weapons trainig! It may at first seem it has nothing to do with anything (since you'll use things like swords and stafs), but it is very, very important!
I see that you don't mention Karate, my first and still a great love. You should consider that too. Any style is OK, as long as you don't end up in some sport and competition oriented school, they will teach you nothing of value in a real situation. Look for, so called, traditional school. Styles: Kaze-ha Shotokan is overall great, Goju-ryu (any flavour) is extremely efective in close combat, Wado-ryu I think even uses some weapon training... Experts say that Kyokushinkai (famous for its full-contact competitions), while may look spectacular in competition, is not very good in a realistic situation (one example: too much high kicks to the head, and very little blocking).
And to conclude this long post, here is what everyone who doesn't know much about Japanese and Chinese MA MUST read if they are looking for a dojo: The Newbie Guide to Martial Arts Training:
http://www.aikidofaq.com/misc/newbie.html
As for the links you listed in the first post:
http://www.chicagomartialartsclasses.com/ --- NO! Don't waste money and time. This is a McDojo. Best MA schools don't need to be voted best by Black Belt magazine or such, good teachers don't wear black outfits calling themselves "grandmaster this-and-that". Again, a big NO!
http://www.chicago-ninjutsu.org/ --- yes, if you want Ninjutsu this is one way to go. Try it, you may like it, but expect to be hit, blindfolded, doing pushups in mudd, runing long distances through snow and stuff like that...
http://team-toro.com/class.html --- couldn't open the page, but I'm no expert in Muai Thai so I wouldn't know anyway.
Good luck!
nik