I am new to linux and java, I have developed an application with Java EE 5 want to host it on linux platform, firstly which flavour should I use CentOS/Ubuntu? which architecture? 32 bit/ 64bit?
and I want vnc support because I cant work on ssh.
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I would definitely recommend 64-bit on a server. As for CentOS/Ubuntu, I would recommend Ubuntu because I prefer debian-based systems to Red Hat-based systems (for many reasons).
I have hosted static and php websites on GoDaddy. I've heard some people complain about GoDaddy, but they were always great for me and at the time, I was comparing prices and GoDaddy was a great value. They have shared hosting plans that include java. Another host that I always hear great things about is Rackspace.
A couple other hosts I've heard about that also have dedicated hosting are Site5 and Dreamhost. I would trust anyone of these hosts with my website. You just have to look and see who has the options you want at the best price.