There’s a wonderful set of Tools that comes bundled with Firefox called ‘Web Developer Tools’. You can use those to figure out what is what and where is where on your layout.
Also, a good way to start troubleshooting is to validate the code for the site. An attempt to validate your code produced 26 errors and where a lot of them are flash-related, there are several that seem to be hinting at the fact that maybe you forgot to close some tags.
So. Go look at your coding and see if you’ve forgotten to close some tags. Don’t just look at the coding on your theme, though! Look at the coding for your POSTS! Posts get translated into code and if you copied and pasted or typed in bad/garbage coding, you can ‘break’ your theme/layout because of it or even break the functionality of your entire site.
I just opened up the site in IE 5 (wooo! older browser than yours!) and according to IE, besides the fact that your right-hand sidebar fails to load any content, you’ve got yourself one random <!--[endif]-->
tag appearing right next to your big RSS icon that’s in your ‘How to Use RSS Feeds’ post.
… Okay. I’m going to take five or ten to read your source code. Quite frankly, it gives me a headache to look at.
You need to clean up your code – especially for such a content-heavy and GUI-heavy site, and BADLY.
I’ll repost again once I’m done reading.