I have had alot of the same issues with my site (
www.shareworld.co.uk), before I done some major sorting out, google and xml-sitemaps.com was indexing around 2500 urls on my site!! (In actual fact I only have 400-500 pages on my site).
The way I tackled the problem was to index my site using xml sitemaps.com (this is free for the basic version) or the link sleuth is also a very good tool. Then you just need to look for duplicate urls or ones you dont want included.
Now if you create a robots.txt file (look it up on Google) you can include in there all the pages/directories that you dont want indexed, that will be a start. - In my experience I found that the "news" module caused a bit of an issue for me - I had about 50 news items (daily market news) and they were linked to from every page on my site - but they had a different link on every page, so they were being seen as thousands of unique urls!!! I made the decision to disallow this particular news group from being indexed and that sorted out the majority of my problems).
Next as Nhaak says:
"2) Browse your site and look for the wrong links. Those that read ...index.php?page=... (if these are the ones you want to have eliminated). Now check your templates and see if something that you have done to show the link requires a parameter, setting or other precondition."
This is important as you may find pages are being indexed twice: once by index.php/page=so-and-so and once as a pretty url:
index.php/group/so-and-so.html So decide if you are using pretty urls or not, then make sure all the links you create within the site follow the same protocol.
Finally, also mentioned previously, use google webmaster tools - submit your sitemaps and check the listed errors - if you resolve all the errors that Google lists then you will be some way towards having an SEO friendly site that Google will concider highly.
Lastly, as an aside, validate your code:
http://validator.w3.org/check?uri=http% ... ne&group=0
You only have a few errors so shouldnt be much work but it will be a big help as far as SEO is concerned.
And also, nice site:)