Vyas,
They can't really be compared directly. Prototype is a kinda light-weight API to weed out browser differences and allow you to use pseudo objects. YUI, which I haven't used much, is known a collection of cool widgets.
GWT on the other hand is a
Java based toolkit that includes RPC, i18n, image tools, code generation, and of course widgets.
The widgets with GWT aren't all that pretty, so some developers use GWT with YUI but creating Java wrapper classes around YUI. GWT allows this through the use of the JavaScript Native Interface (JSNI).
Rob