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You'll find hosts using debian, centos, red hat and freebsd.
There can will always be small differences in configuring and/or file locations per distro. But once you get a hold of it, a different distro wont be hard to manage. Ubuntu is noob friendly but maybe not wide used by hosting companies.
Why not check what your favorite host uses and try to learn that. Gives you double advantage ;-)
Else go for freebsd or debian, but thats only my 2 cents ;-)
Good luck
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