strategy for site with multiple entry points?

personal sites are often eclectic

[RFranzen]

I just read the thread about interlinking consistency at:

* [webmasterworld.com...]

Basically it says to be consistent in what you use as your base URL. Choose a form and stick to it, whether it be:

* [mysite.com...]
* [mysite.com...]
* [mysite.com...]
* [mysite.com...]
* or even just "/" or "/index.html"

On my personal site I have been inconsistent. I never use the "www" prefix (although the hosting service does support it as an alias). But sometimes I use the "/index.html" file name, and sometimes I use the site (or directory) name without including the default filename. I'm planning on fixing the site to consistently leave off the default filename. Great advice and info in the previous thread -- thanks to all participants!

However, the thread's discussion focused on integrated domains. Mine is eclectic with multiple semi-logical entry points. In fact my most popular page isn't even a default; it is something like "mysite.com/graphics/somethingNeat.html".

Some of my subdirectory hierarchies function as independent sites which just happen to be co-located within the same domain. Are there hidden gotcha's about such an arrangement? Could Google or other search engines take a dislike to heavy interlinkages to a subdirectory entry point? To me it is obvious each entry point should be treated as a site in and of itself. I'm just worried that at some point a search engine algorithm will decide Rich is cheating.

-- Rich