I am working on this website:

http://www.djcarchitect.com/portfolio/currentprojects.html

I want to add about 30 extra projects on the left side, under Current projects. I want this to be able to scroll vertically, so that it doesn't stretch my page down. I tried using an iFrame for the links, but whenever I clicked on a link inside the iframe, it opened up the target page within the iframe as well (it was all smushed).

I would ideally like to have a ton of those links, be able to scroll vertically, and open in the same window without adding more windows for the people on the site. Any help please? Thank you!

You need to target the right frame.
http://htmlhelp.com/reference/html40/values.html#frametarget

But since you only have one frame (I assume) you 'll need to inlude the iframe on every page. Since frames aren't that cool anyway, you can just as well include the navigation directly on each page and make it scroll with CSS 'overflow'.
http://www.w3.org/TR/CSS2/visufx.html#propdef-overflow