Data conversion
format of data from data logger to format used in modelling software
format of GIS to format used in modelling software (or vice-versa)
Structuring your work
separate source data and 'working data' - automatic conversion by a program!
Developing models
All modelling software (e.g. PCRaster) has restrictions regarding functions provided
Using a programming language results in faster models (sometimes)
Other reasons
Other software, e.g. developing a www site, creating a graphical user interface