I have a domain name I'm developing. I registered the .com/.net/.org for the name.

Should I:
1) Forward the .net/.org to the .com
2) Point the .net/.org to the .com directory using the DNS which leaves thesitename.net in the browser

How will each affect/help the indexing of the site/usability and should I let it default to index.php or use index.htm forwarded to index.php.

:dunce:

IMO, go with #2, because it just makes it look more professional.
(for example, look at: pscode.com/planet-source-code.com/planetsourcecode.com because it does exactly what you talk about in #2)

Also- let it default to index.php because, again, it looks more professional.

Well, .ORG domains index better for some strange reason, even when they mirror a .com or net domain name. But the truth is that it doesn't matter what domain extension you use, as long as your site and it's content are conducted professionally.