I'm a sea kayaker, and I pretty much agree with hikermor's comments. Sea kayaks are much better if you will encounter rough water or wind. While some canoists can handle some serious rough water, this takes a great deal of skill and training. Ultimately, an open canoe just does not handle rough water nearly as well as a decked kayak. Also, canoes sit higher in the water than kayaks, and thus are much more susceptable to being pushed around by the wind.

That being said, I believe Canoedogs is correct that canoes are easier to portage (especially on solo trips). Also, canoes can generally carry more stuff. For longer trips, as Canoedogs mentions, a canoe has some real advantages in the amount of food and gear one can carry.

Ultimately, it comes down to a personal choice. If you are planning on travel in big open water then a sea kayak is probably the best option. On lakes and rivers, where one might need to do a lot of portaging, the canoe might be the better choice. Either way, make sure you ALWAYS WEAR a good PFD, develop some skills with your boat of choice, and exercise reasonable caution and common sense.

Have fun on the water! Some of my most enjoyable days have been spent "messing around in boats".