A hybrid system seems to usually work best. There are also several organizational systems. When designing your web site, consider your user. A web site should work like a reference interview. Each step should help the user self interview and should afford the user access to data tools appropriate for the user's information needs.
People usually ask for information by topic.
The information provider can choose to offer various means to data to allow the user greater flexibility or they can choose to shepherd the user to the information. Another important factor to consider is how you label your choices. Also, do not underestimate the likelihood a user will get confused. Give them tips or alternatives where you find that people may get confused. Also icons tend to be VERY confusing.