I am using v.2.1.0.1b SEF. There are a few problems I see from an SEO point of view (not that I'm an expert - more lucky I have a few pages and site that perform well for niche markets!).

I don't like the fact that Google indexes the out.php files... but that's more a glitch of Google than any particular coding practice (I have the same 'problem' for a topsite script I cobbled together).

For an example of the duplicate output I am trying to avoid see:
http://www.google.co.nz/search?q=site%3Aspeakspanishlikeagringo.com%2Fdir%2Fdirectory%2Fadd.html

with duplicate title / description output:

Add Speak Spanish Like A Gringo Directory
Add Speak Spanish Like A Gringo Directory uses DewNewPHPLinks an open source directory script from Dew-Code.com.

and
http://www.google.co.nz/search?q=site%3Aspeakspanishlikeagringo.com%2Fdir%2Fdirectory%2Fowner.html

with duplicate title / description output:

Owner Speak Spanish Like A Gringo Directory
Owner Speak Spanish Like A Gringo Directory uses DewNewPHPLinks an open source directory script from Dew-Code.com.

I have adapted my the directory (php) script for one of my sites to add noindex to the owner.html and later will update the add.html to only index add.html and not have all the add.html?PID=xxx indexed.

For a while Google was heavily penalizing web/link directories, as so many had popped up just duplicating DMOZ (for e.g.). I think they still penalize, especially if a page is clear just a collection of links - hence I feel the need to add the directory description to each category page output.

Cheers,
Graeme