What's best depends on you.

If you can code a few python scripts, use boto http://code.google.com/p/boto

If that looks too scary but you can handle ruby then consider Capazon and Capistrano - http://capazon.rubyforge.org and http://capify.org/

If none of this command line / script stuff is your thing then you may want to look at some web admin tools like Virtualmin (http://www.virtualmin.com) that support EC2.