I will be doing siloing as part of my seo strategy. This means that I will need a more complex yet clean internal linking structure. The home page will need all the main categories linked to and then the categories will need to link to each of their respective sub categories. (and likely one more layer deep). Additionally I am looking for software that leaves clean links and is very seo friendly in many other ways (keywords in url, etc.). Which content management software do you advise and why? (Joomla, wordpress, pligg, drupal, others?)
Wordpress is the best CMS for SEO with just 3 or 4 plugins installed. however drupal,joomla can be made seo friendly with tweaks.
Wordpress hands down. It's so easy to customize it to exactly how you want it. I've had some experience with Joomla, but I much more prefer Wordpress.
You can also try some other alternative. I heard about SEO toaster, which is said to be a content management system that is highly optimized for seo purposes. I havent used it personally, and I am not affiliated with it. Just sayin' you may want to give it a try if it will work out for you.
Btw, I went with wordpress. Very happy with it. Took a lot of tweaking to make it as SEO as I wanted it but wasn't that hard at all and I believe it's going to have great results and save a lot of time over hand coding each page. Strongly suggest this for others. (my site is NOT a blog, its made of pages instead of posts)