For seo purposes is it bad practice to link to your home page as index.htm, index.asp or whatever it is? Is it better to have internal links pointing to "http://www.domain.com" or "./"? What I'm getting at is does Google count www.domain.com and www.domain.com/index.htm as 2 seperate pages?
you should use one uniform URL for building backlinks. if you use domain name, /, and index.htm for link building, then you will have PR leak which is not good for ranking. albacklinks will need to direct to a single url. its a wide idea to setup a 301 redirection to redirect index.htm, www.domain.com, domain.com (without www) and whatevre other variation of url you are using to a single url like www.domian.com. this way your main domain gets credited for all the backlinks
Yes search engine crawler treat them as two different pages you can resolve this is issue by implementing a 301 redirect to your preferred domain. The other method that you can use is adding canonical link element this will tell search engine what is your preferred domain and other domains will be ignored by it.