The primary issue for us in selecting Zendesk is that we needed a product that was flexible enough to support our very specific model. Our business generates parent Purchase Orders with a series of child Purchase orders associated with each parent. We needed a ticketing system that could support this structure and Zendesk is the only one we found that could do this.
Zendesk was also one of the less expensive systems we looked at. Competitive systems like Zoho and Desk.com were significantly more expensive - especially Desk which has a usage-based pricing model. Zendesk's pricing model is based on the number of administrative licenses with an unlimited number of user licenses underneath that.
The API was clean and easy-to-use. We used the API to integrate the product with our website and with our home-grown CRM system.
There were some website integration issues. It would have been nice to allow our users to login to the customer portal and be automatically logged-in to Zendesk at the same time. Instead, customers had to log in separately to Zendesk.
One of the big advantages was being able to get Microsoft Outlook out of the equation. We have a central place for everyone to see tickets and Zendesk has it's own email engine which eliminated to need to use a separate systems for communicating with customers.
The system also helped a lot in managing our KPIs. We were able to measure things like time required to resolve tickets to enforce SLAs with our vendors and ultimately provide better service to our customers.
Zendesk - not surprisingly - has a great support team. They were very helpful and easy to work with. Our pre-sales contact at the company also remained a great resource even after the sale had been made.