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What exactly do you want to customise?
If you want to modify the presentation and structure, all self respecting CMS's run on (x)HTML and CSS templates which you can change to your hearts content.
If you want to modify functionality, virtually all CMS's have a system that you can tap into and use to write your own custom modifications.
There isn't really a "best" one since every project will have it's own specific needs - CMS ABC might be suitable for one site, but not the next.
The best solution for you is to look at a dozen or so CMS's (search these forums for ideas) and see what they're capable of, both out of the box and with modifications. Find the ones you can understand and use, then pick the most appropriate one for your next project.
Last edited by blue-dreamer; 02-01-2009 at 04:50 PM..
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