I noticed something odd about my home page URL and its associated PageRank and I'm not sure if it hurts my optimization efforts.

OPTION 1: When I type in my URL as http://www.yourdomain.com, I see that the page has a 7 for PageRank.

OPTION 2: Our logo in the upper left corner of our home page points to http://www.yourdomain.com/index.html. When you click the logo, the page I arrive on (which has the exact same layout) has a PageRank of 4.

OPTION 3: If I type the home page URL in as yourdomain.com (no http://www) and hit return, the page I arrive on has a PageRank of 5.

Would my PageRank for link option #1 be better overall if I made our logo point to http://www.yourdomain.com? I've seen all three of our options show up in Google results and I am worried that I am "splitting the PageRank" of our brand name by having the index.html link on the home page.

IMHO, yes you are. You should combine the URLs into one.

I would change the graphic to point to www.domain.com and then set up 301 redirects in your htaccess file pointing all versions of your URL to www.domain.com.

http://www.webmasterworld.com/forum92/1078.htm will provide the syntax.