I am 19 and fell in love with cycling this past summer. I a currently a sophomore in college, and have quite a bit of time to train/workout. The only problem is, I am not sure what would be the best thing to do for me. I could probably do an hour or two a day, right now I work out about an hour a day. I either swim, run, do machines at the gym, or of course spend time riding on the trainer.
I am 6'4" and about 160 lbs, so losing weight is not really important to me, in fact I would love to gain some muscle mass to become stronger.

Any suggestions?
I am not just looking to get in great cycling shape, but also great shape in general.

I figure, if I have a bunch of free time, I should make the most of it and not just blindly workout every day

To not "blindly" work out you need a specific goal. To most people "blindly working out" provides the benefit of general fitness increases. If you feel you cannot progress any further with doing what you are doing, you need to pick a goal that relates to your cycling, and take it from there.
Great shape in general would imply that, while you would be fit, not all of your fitness would relate directly to cycling, and some of said fitness (lots of upper body mass, maybe?) may even be detrimental to your cycling.
So what do you think you REALLY want to see improve in your riding?

Well, if you want to gain weight and muscle mass, lots of cycling is not for you. I don't know if you just want to work on your cardio or start racing. I would suggest going over to the body building forums and checking out Rip-toes starting strength. If you're serious about cycling then I would get the cyclists training bible, and that will help you build a guided workout plan for the whole year.

I am serious about cycling, as serious as I can be after only riding a road bike for about 6 months. I would say my main end goal would be to be in great aerobic shape and eventually able to race. Maybe I am just a bit anxious because I have no experience, I just want to hit the ground running (as much as I can be with being so novice) come springtime/throughout the summer.

What is this cyclists training bible?
...i know, use the search function, i will right after this

I was the same age when I bought my first real road bike. Mostly you need to ride as much as possible, except that you probably can't much right now because there's snow, right?

Yes, Friel's The Cyclist's Training Bible.

I'd park the swimming and running for now. Ride your trainer and work out at the gym. At the gym, Friel has you start doing circuits with 3 sets of 30 on about 7 different exercises. I recommend that very highly. You do that 2-3 times per week for a few months and it will make a major difference. Ignore the bodybuilders.

The StepMill, other Stairmaster machines, and elliptical trainers are also good. Spin classes are great if your gym has them. Running stairs is also good. Stadiums or tall buildings.

You're very tall. Be sure your bike fits you properly. Manufactured bikes weren't developed with you in mind. Even 180 cranks are too short for you. You may eventually want a custom frame.