There are several new interfaces in ArcGIS 9.3 related to 3D GIS that are very handy and provide some really useful new functionality. Here's a summary of the the most important ones to learn as you update your application:
ICurve3D - has several methods for getting 3D length of a curve, 3D subcurves, etc.
IVolume - gets the volume of a multipatch.
IImport3DFile - useful for loading Sketchup v6 and Collada 1.4 files.
ISegmentZ2 - this interface adds the ability to densify a 3D segment.
IProximityOperator3D - this interface is just like IProximityOperator except that it allows you to compute the minimal 3D distance and returns the nearest 3D point.
IRelationalOperator3D - this interface has one method for determining if two geometries share no points in common.