Folders vs flat URL structure
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Hi Muhammed,
It really just depends, but ultimately it's what you think it's best for the user experience. The below Matt Cutts video basically answers your exact question and he says it doesn't effect search rankings.
http://www.youtube.com/watch?v=971qGsTPs8M#t=100
I would go with the filepath though.
www.sitename.com/used-cars/honda-civic-2013-for-sale/
Hope this helps!
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Folders and directories also aid search engine crawlers with helping them understand your sites structure and hierarchy better, as in many sites this is very appropriate. Also for user experience this can provide help.
Some users with blog type websites have also experienced slow performance with large quantities of pages under the same directory.
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Like the other two respondents have said, think about users. However, also think about your developers, future SEOs, spiders, etc... If it were me I'd go with www.sitename.com/used-cars/honda/civic/2013/. That taxonomy makes a lot of sense to me. It is more logical and useful than a completely flat architecture. For instance, I could easily see how many pages were indexed from the /honda/ directory Vs the /ford/ directory, or any others. I could easily segment my sitemaps by manufacturer, model or year. I could work with the database easier to perform a whole variety of tasks.
I think search engine spiders probably would feel the same way if they had feelings.

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In addition to seeing the pages indexed, the segmentation works just as well in your analytics. You can see which make is getting the most traffic, which has the highest bounce rate, etc. You could even filter on just /2013/ and look across all of the 2013 cars you have to see how they are performing compared to the /2012/ cars.