The most significant difference is that Java JXL does not support the Excel 2007+ ".xlsx" format; it only supports the old BIFF (binary) ".xls" format. Apache POI supports both with a common design.
JXL only supports certain text rotations: horizontal/vertical, +/- 45 degrees, and stacked; Apache POI supports any integer number of degrees plus stacked.
Additionally, the Java portion of the JXL API was last updated in 2009 (3 years, 4 months ago as I write this), although it looks like there is a C# API. Apache POI is actively maintained.
