That is usually a personal preference. Usually I tell people make a list of everything a software must have as well as must not and then make some calls to do some online demos of the products.
For example for me I did not want to host the software myself I wanted it web based but also wanted to have access to download all my data at any time. Some people want to host/purchase the software and run it in house. Cost is a concern for many but keep in mind some of the cheaper software is difficult or impossible to move over to another provider if you ever change your mind to a diffrent ATS system down the road. Newer companies trying to save money may use a cheaper system for a year inputting all types of data and realize that when they decide to upgrade it ends up costing them twice as much because the data migration is so costly. Just points to consider but you can only gain your likes and dislikes by demoing the products with some of the ATS providers. If one was "the best" for everyone then there wouldn't be so many providers in business.
There have been a ton of discussions about how people like or dislike thier current ATS systems over on www.RecruitingBlogs.com. If you go on the site click Community at the top and then up in the top right hand corner will be a search box where you might put in ATS or Applicant Tracking as a search and will see many discussions over the past year. ERE.net has some of the same types of discussions though the postings on the RBC network are more candid responses.
Some of the more popular ATS systems to start are Bullhorn, Akken, SendOuts, MaxHire and PCRecruiter. If you need individual sales contacts for any please feel free to contact me. shannon@waltonsearch.com
Sorry everyone...I just realized I answered Paul's question from a staffing firm perspective. Force of habit. If anyone has any recommendations from a company perspective please add to the list.