Satya,

In future, please elaborate on your questions and clarify what all fact finding you've done from your end instead of just posting a generic question in the forums.

I'll provide some quick background information

Custom Apps

Custom apps can be either free-standing apps you create with Salesforce Mobile SDK or browser apps using plain HTML5 and JQueryMobile/Ajax. With custom apps, you can:Define a custom user experience.
Access Salesforce data using REST APIs in native and hybrid local apps, or with Visualforce in hybrid apps usingJavaScript Remoting. In HTML5 apps, do the same using JQueryMobile and Ajax.
Brand your user interface for customer-facing exposure.
Create standalone mobile apps, either with native APIs using Java for Android or Objective-C for iOS, or through a hybrid container using JavaScript and HTML5 (Mobile SDK only).
Distribute apps through mobile industry channels, such as the Apple App Store or Google Play (Mobile SDK only).
Configure and control complex offline behavior (Mobile SDK only).
Use push notifications (available for Mobile SDK native apps only).
Design a custom security container using your own OAuth module (Mobile SDK only).

Force.com Sites

Force.com Sites lets you create public web applications and web sites that run natively on Force.com - under your own domain. Force.com Sites lets you easily extend the reach of your existing applications to new, external audiences, and your site visitors don't need to authenticate to view your pages. In fact, if you're already using Visualforce to create your user interfaces, it's a simple matter of bundling them into a Force.com Site to create a public web application.

Some key features of Force.com Sites include:

The Force.com Sites technology utilizes Visualforce, the platform framework for building and deploying custom user interfaces.
The URL for each site can use your unique Force.com domain or your own branded domain.
Force.com Sites can easily generate Atom syndication feeds based on SOQL queries.
Public access settings control which database objects and fields are accessible to visitors.
You can easily use the built-in content distribution network integration to cache pages.

Please refer to the official documentation for further details and post another thread if you have specific queries.

If my answer helps resolve your query, please mark it as the 'Best Answer' & upvote it to benefit others and improve the overall quality of Discussion Forums.

Gaurav Kheterpal
Certified Force.com Developer| Salesforce Mobile Evangelist| Developer Forums Moderator| Dreamforce Speaker