What URLs do you link to within your own site? Do they look neat and tidy, or do they have long strings of meaningless nonsense?
A good solution is to use the <link canonical> tag. On each page, include in the <head> a tag along the lines of:
<link rel="canonical" href="http://website.com/example/page.htm">
, where the address given is the address that you want Google to index for that page.