Well I know the first thing that people are saying is, “Oh no not another distro debate.” I myself hate these debates so I am going to try my best to not make this one. My purpose here is to explain the difference between the two. One of the things Linux offers is a lot of choices of distributions. There is no regulations on who can create one. For more on that you should visit Distro Watch.
Gentoo is an operating system that beginners should not get into unless you like to live dangerous. Unlike most distro’s it is not a click next installer. You have to edit configuration files and work via the command line. Now I know that Gentoo is working on a GUI installer so that might make installing a little bit easier.
The one of the things I do like is that you can set the USE flag for installing applications. What I mean by this is you can tell Gentoo when install an application what you want to build with it. For example you can build apache without MySQL support. So if you wanted to add mysql support you just have to add the word mysql to the USE section in the make.conf. Now one of the con’s of Gentoo is that all applications from portage (the system Gentoo uses to install applications) are built via source. So on some systems to install KDE it takes over 10 hours. This of course can depend on your system. So I would recommend that you try installing Gentoo in a Virtual Machine first to see how you like it or of course you can try the Live CD.
Ubuntu to me is the Windows of the Linux world. You install it by answering some questions, hitting next and all the work is done for you. Ubuntu is the distro I recommend for the beginner to the Linux world. There is hardly no configuration change at all. I have rarely seen an install that you had to mess with configuration files to get it to work.
The apt-get system is like portage but it does not build the application’s from source. The only con that I can come up with is that it is too simple. This is a preference to me. Let me explain this logic here. There was a time that installing Linux was not an easy task. Everyone could not do it. Gentoo is one of those examples. When you could install it you felt good about it. When you install Windows you feel nothing. This is how I feel about Ubuntu. But being easy is need because then Linux has no chance of overtaking Windows. Well that is for another blog post at another time. In conclusion I believe if you are new to the Linux world you should try using Ubuntu and mess around with that and get your feet wet. Then when you are ready for a challenge and ready to take the next step, install Gentoo.