It depends on what type of help desk system you wish to build. A proper and complete IT Service helpdesk system for a medium or large company comprises of the following subsystems:
1) A fault logging and tracking system. This system identifies the user, issues a fault ticket, and logs a history of faults/requests submitted by the user. There are many off the shelf applications that do this
2) A knowledgebase. This is used to log commonly encountered faults, so that admin staff do not need to reinvent the wheel when diagnosing faults. There are off the shelf applications that do this
3) Self help systems. This is where web pages are developed to help users log faults / requests, or process common requests online. For large companies, such systems are imperative. The most commonly submitted type of fault is a LAN password reset. For large organizations, it is important that an automated LAN password reset system be built, and customers forced to use it. In my organization, I built such a tool several years ago. It processes over 10,000 password resets/account unlocks in a month.
4) Help desk fault diagnosis tool. In my organization we have a custom built tool that retrieves as much information about a user, and presents it in a simple interface for LAN admin staff to use. Such information includes the users details, LAN accounts, workstation used, whether the LAN accounts are locked, etc. It relies on a backend database of user information, and whatever other data can be retrieved from the network. Its a bit hard to explain here, but it is a very well used tool in our organization.
5) Systems status monitor. This is a web based tool that lists any major faults encountered, such as a server or network outage. This is visible by LAN staff and users alike. Its purpose is to stop large amounts of users ringing the helpdesk to report what is essentially the same fault.
There are more systems that can be mentioned, but these are the most important. Good luck.