Just wanted people's opinions on this, its a relativley new site, there was content on the site previously but it changed completely in the past few months, and I have really launched the site and began updating it on a near daily basis. It is not a commercial site, so I have never been bothered too much about google traffic.

However I have been wanting to at least get it indexed well, for the past few weeks indexed pages have shown in google for a day then dissapeared completely and not reappearing. Now some pages are showing up, but all as supplemental. At the same time I did realise also that I had completely mucked up the HTML when porting the w3c valid template on the toeh CMS i use.
So I decided to sharpen up the template a bit and fix the errors, so I thought why not make it google friendly too, the things I have removed are as follows;
One of those "tag cloud" things at the bottom of every article page (contained about 100 links at the time all internal, it got out of hand lol) this was something I thought was good for users, but really thought google might not like it.
A <span> that had font-size: 0px; silly me for sticking one of those stat websites links on my site and not checking it (durr) google analytics and my daily webalizer dont cut it for me.
Obviously most pages are now 100% valid.
Took a lot of links from the navigation div. Put nofollow on links that really werent important to the spidering process.