Crashed; now have blank spaces in dock

Hello
I got my iMac in december of 2007, and I havent had any major problems with it until 2 days ago. I was working on a project, and I downloaded a font (which is the only think i can target it to) and when i tried to use the font, my iMac froze. I waited a very long time, tried to force quit, and nothing was working. I decided to press the power button, and when i tried to turn it back on, I could only get as far as the blue screen with the apple symbol , and then i got the circle with the line through it. I tried ******** it down via the power button a few times after that, and at some point i couldnt even get to the apple symbol. I tried some of the suggestions in my Everything Mac book, and none of them worked until I did an apple hardware test. That showed that there was no problems, and soon after, it started up again. The only thing is, now there are blank spaces on my dock where some of my applications used to be..... but i can still access them by pressing their blank spaces. alone with 3 of my applications acting this way, my trash can and my dashboard is doing the same thing. (where dashboard was, there is a piece of the white square that the whole dock rest on that appears to be 'cut out')
Im afraid that this might be a software problem with the operating system, and that I may have to backup my 70G of files and reinstall.
Please help me understand what has happened, what is going on, and what my options are. I hope to god i wont have to pay someone to fix this for me, but ya gotta do what ya gotta do.

This MAY have been prevented by doing these steps prior to any update, but try them now...
Boot from the Install CD/DVD then after you choose your language, a Menubar will show up top, find Disk Utility and run it from there.
Verify & Repair if necessary first, then Permissions.
Using Disk Utility in Mac OS X 10.4.3 or later to verify or repair disks...
http://docs.info.apple.com/article.html?artnum=302672
About Disk Utility's Repair Disk Permissions feature...
http://docs.info.apple.com/article.html?artnum=25751
There's plenty more we can do, but 1st these need to be in order.

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