well its hard to suggest somthing without first knowing what your exact needs are..

1. WHMCS
If you are going to be selling products, services, etc. I would definitely recommend using whmcs. It has a built in support center which works nicely with the products/services.. Another good thing about it is it can integrate right into your server, allowing server accounts to be created and modified from within whmcs. Dozens of payment processors (paypal, intuit merchant services, authorize.net, etc..) are included as well as dozens of domain registrars (your clients can buy domains from your website and manage those domains from within your website). If you happen to host with Hostgator you can get WHMCS free.

1. Cerberus Helpdesk
This is a great standalone support center.. It has as many features as you can possibly need and is free if you are going to have 3 admins or less. I recommend this if you dont want to sell products/services on your website.

EDIT: I have had tons of experience with both of the above support centers.. If you want I can give you live examples of the front-end, client-size, knowledgebases, etc. for both systems.. Or create you a sample ticket to show you functionality.. Your choice of a support center can greatly effect your business down the road.