Maria,
If you are using ArcGIS 9.3 I'm not sure if there is an easy way to do it within ModelBuilder. I believe in 10.0 ESRI has introduced some enhancements, including "if statements".
My recommendation would be to convert your model to a Python script tool.
First, I would export your model to Python. (If you are not familiar with Python programming there are plenty of exmaples in the ArcGIS Desktop help to get you going. Python is pretty straightforward and easy to pick up.)
Next, add some simple logic to test the input parameters (i.e. csv, shp, raster) to decide which part of the code to run next.
Finally, create a tool for your script in ArcToolbox.
I hope that helps,
Joel