Are sites with the .php extension worth linking with?

Will they be spidered if they do not have an html extension?

Check to see if the page is indexed by the search engine. If it is, then absolutely, it is an effective link. Google in particular indexes Word files (.doc) and Acrobat files (.pdf) in addtion to HTML. Moreover, php, asp, and jsp files just create HTML output so by the time a browser or Google’s spider sees the page there is no difference. If you take a look at the HTTP headers for these pages (you can do this with OptiLink) you will notice that the content type is text/html just like any "regular" HTML file. The only thing unusual is the page filename extension which bothers Google not in the least.

For really clever folks, you can’t even know what was executed on the server to produce HTML output. For example. it is trivial to configure a server to execute PHP when .html files are served — one line in an .htaccess file is all that is required, so the filename extension really and truly does not matter. The only thing that browsers and spiders can, and do, trust is the Content-type field in the HTTP header.

Are high keyword densities penalized?

When you see really high on-page keyword densities in OptiLink you’ll probably find the the pages are framed and the noframes tag has a very limited string of text in it. Since it is only the noframes tag that the spider is seeing, the keyword density can be very high. But at Google at least there does not appear to be a threshold where some penalty gets imposed. In fact, beyond the title tag, Google does not appear to care about on-page factors at all. At Google, linking is king.

Does Google frown upon pages of the same domain cross linking with each other?

Isn’t this just a normal site navbar? How would a human use a site that did not have such linking?

Or maybe you are referring to multiple subdomains linking to another, see aboutus.com and howstuffworks.com for two very large, very well constructed, very heavily cross-linked and very well ranked examples.

No, it doesn’t look like there’s any frowning involved. 😉

Will I be penalized for linking to non related sites?

All outbound links are evil (because they bleed PR), but generally a necessary evil, and where they go does not in the least matter.

Is a link from an unrelated site a bad thing?

All inbound links are good links. Every link from a page that is actually in the Google index will award some amount of PageRank, no matter how small, and will provide Link Reputation through the text that is used with the link. Just be sure to get the correct link text in the links that point to your pages.

Should my inbound links use a single phrase or could I use 2 phrases?

I have not been able to measure any difference between these two stategies. On purely theoretical grounds the single focus linking should edge out the other approach all other things being equal. But on the other hand, no page lives on a single search phrase alone. And furthermore, the difference between the two I am certain is very minor. Sooo, I would think that multiple related terms is okay, and possibly even better.

That said, I would use a "noise word" connective like so: "cell phones and phone accessories" simply because it reads better to humans than "cell phones, phone accessories".

In all cases, make sure the phrase has no intervening words, like "cell phone plans and accessories" does not work as well for both phrases as does "cell phone plans and cell phone accessories" simply because the engines like to see the phrase contiguous instead of interrupted by other words.

What is optimal page keyword weight and what is too high?

There is no right answer to this other than to measure what is currently working in the search engines — that’s what OptiLink is for. At Google, the on-page density carries almost no importance. As long as you get the keywords in the title tag, just about every other aspect of ranking is Link Reputation analysis or PageRank.

Does title or body of a page determine its “topic” to the SE’s?

Probably both, with title being the more important of the two. Google appears to rely almost exclusively on the title in terms of on-page factors.

Using a graphical “home” link on every page is common practice. Do you recommend an alternative?

There are a number of techniques I recommend to clients depending on specifics, but, while it may look good, in no case is a graphical link a good ranking tool. Because the engines do not appear to use the alt text of an image to influence Link Reputation, the image link serves to dilute the reputation of the targeted page. I would always make these nofollow links and provide a separate text link, or include text along with the image in the same link — that does appear to work — and then style it using CSS so it looks decent.

How does one develop PageRank for all their 40 or so internal pages, as well as their homepage?

It is pages themselves that actually create PageRank. Links just spread it around. So to get high PR on one page, will require that you give up PR somewhere else, or you get links from other sites. There is no linking strategy that will "create" PR.

That said, the linking structure you use is critical to controlling where PR gets concentrated. This is the subject of the Mastering PageRank video.