Hello,

Will Google and other SE's see all links to site.com and all links to site.com/index.php as the same?

For example: there are 1000 links pointing to http://www.site.com/ and 500 links poitning to http://www.site.com/index.php , would google see site.com as having 1000 links or 1500 links? (lets just say 100% of links are counted)

So should i promote only one of the options or would it really not matter anyway?

Ty

They are seen as seperate URLs and therefore as possible duplicates. The end result is that you would be likely to lose the value of your internal links to the "home" page, leading to a potential disaster, as your own site links are the only ones that you can be sure are given any real value.

be consistent and only link to the root of the site or sub-directories, NOT to the pagename.

Just like Chis said.

You're best bet is to do a 301 (permanent redirect) from one to the other. I like having things pointing at the domain itself without the index.php file name.

I have to do both. I have a web directory in my root folder that uses mod_rewrite to make SE frindly URL's, so if i try to link to the forum with domain.com/forum it looks for a catagory called "forum" in the directory and throws back a database error, So im having to always link to index.php for deep directories

But the rule of thumb is keep things consistent and always pointing to the same URL.