Well, let me explain this briefly:
1.I want to build a website that provides location based services, like http://fireeagle.yahoo.net/ .
2.I guess most of these services have something do with longitude and latitude.
3.Is there any particular database/datastore/data structures fit well for such apps? I mean easy to store longitude, latitude and easy to compute or easy to use.
I am new to this and any feedbacks are welcome
Spatial extensions to relational database systems provide storage and indexed access the geography/geometry datatypes. They allow you to perform spatial joins and all sorts of spatial queries. In short, they are exactly what you need.
If you are using the open source stack I would recommend PostGIS, the spatial extension to Postgresql. If you are using the MS stack, try the spatial extensions to SQL Server 2008.