There are definitely a lot of things to take into consideration when it comes to picking the help desk that is right for you.  TechRepublic has done an excellent article on this very topic that I would like to share with all of you:

Here is just a little taste before you dive into the real deal:

The consulting firm I work for recently asked me to find a solution to meet our help desk needs. Specific qualifications had to be met for this help desk system to become “the one.” I assumed the task would be simple — after all, I’ve spent the last 10 years covering software of all sorts, including help desk tools. The reality was much different. There are a LOT of help desk systems available. So many, I quickly realized just how challenging the selection would be.

Read the rest of 10 things to consider when choosing a help desk system.

They have touched upon many important factors here.  Making it easy, branding, ticket management, web interface, personalization, security, features and budget play a key role.  One help desk system I know of that meets all the qualifications is TremenDesk.