I have a problem that has just started, and have not had this issue before. I have used the "Spatial Join" tool dozens of times with the same feature class(s). However, this time something is preventing me from doing it. I am trying to put a Point Feature Class in the "Join Features" to join to the Target Feature Class (Polygon). I can add the polygon feature class into the target feature but no matter what route I take - it will not allow me to select the specific point feature class I need. Whats going on and how do I fix this? Im trying to get it to say all these points that are within the polygon region - show in the output feature class. Like I've said - i have used this tool dozens of times before with the same feature classes.
Can you make sure that the feature class you are trying to add is not corrupted? Maybe you could restore the geodatabase if you have a back-up just to check that the problem pertains even with the previous version of the feature class. Or just copy and paste the point feature class you have problems with and then use the newly copied one instead.
If you are drag-and-drop the map layer from the Table of Contents in ArcMap to the tool dialog box, maybe you could try browsing to a feature class stored in the geodatabase instead. I guess you know that you can perform spatial join either from the right-click the layer > Joins and Relates > Join or by using the GP Tool - Spatial Join in the Analysis toolbox (http://help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//00080000000q000000.htm). Test both methods to see if could make any difference.
Have you performed any recent upgrades of the software, any service packs? Any processing of the geodatabase you work with?
Make sure that the match option you are using is valid for the input combination. For example, the tool won't let you do polygons WITHIN points; you can only do polygons CONTAINS points or points WITHIN polygons.