Choosing database for storing spatial data?

PostGIS based on PostgreSQL is a popular database for GIS.

I haven't used it much myself, but a pro is that it's open source and that many other GIS uses it so it have an active GIS community.

SQL Server 2008 comes with geospatial capabilities in-built. Even the free Express Edition supports the full geospatial features, as far as I know.

Further reading:

• SQL Server 2008 Spatial Data
• MSDN: Working with Spatial Data (Database Engine)
• MSDN: Working with Spatial Indexes (Database Engine)
• Basic example from Stack Overflow

Although my vote would go for PostGIS as well, SpatiaLite extension for SQLite might be woth looking at as a lightweight alternative.