I run a small SEO company and have few hundred clients. I am wondering if anyone can suggest me a shopping cart from where i can manage client orders, update/upload various reports, invoice them, manage support tickets etc?
Magento, CRE Loaded, X-Cart, Zen Cart - most of modern shopping carts can do that. Also, check this out - http://magneticone.com/store - you can find software that makes shopping cart management easier.
X-cart would be my choice. I was running a couple of ecommerce sites with x-cart - easy to use, easy to install.
If you taking orders manually, through phone etc... you can use an accounting system like Sql-ledger, phpaccount, weberp etc... or if you are looking for clients to place orders online and track orders.. I recommed, oscommerce , creloaded or Zen cart.