We prefer the bare domain name -- that gives you more flexibility to rearrange the site later, without having to wait for the directory listing to be changed. Of course, for one reason or another the bare name doesn't always work, and we would list "index.htm" or "homepage.php" or whatever, if necessary.
What we DON'T like is a barename like "http://widget-stuffed-keywords.com" that redirects to "http://geocities.com/joes-gadgets/widgets/index.htm" or even to "http://joes-gadgets.co.uk/widgets/". We have editors and other tools to eliminate that kind of thing.
Occasionally an editor or other tool makes a mistake, and (seeing that widgets.com redirects to widgets.com/index.htm), changes the listing to add the index.htm -- it is, after all, a kind of redirection. But in reality it is an acceptable (OK, THE acceptable) kind of redirection.
The same principle applies to deeplinks: we'd rather list
http://joes-gadgets.com/widgets/ than
http://joes-gadgets.com/widgets/index.htm but it's more important to use whichever URL actually works.
