In a post Chris's site, he linked to an PDF of a webpage containing an Eggnog recipe. Seeing this, I finally saw a solution to saving webpages in my note keeping program. Links to the referenced pages weren't necessarily going to be around next time I wanted to visit the page, and saving a webpage as an HTML file is always lossy or messy. Chris used the full version of Adobe Acrobat, which I don't have, so I tried looking for a free option to convert webpages to PDF's.
The best thing I've found so far for Windows is htmldoc. Note that you'll have to search for the compiled binary, as the author only provides the source for free. I was having problems getting the program to work through a proxy, so until I get that figured out, I'll be using the pdf-o-matic that the software's author provides on its website. I've only run into one website that didn't translate well, due to very wide images, but I've been able to get over it.
I'm sure there's probably a better free option out there, but I haven't found it yet, and I'd appreciate any suggestions.