Right-clicking on an object does not select or deselect it for almost all objects. Additionally, box select does not select objects. The only exceptions are lamps and speakers, which are both selected correctly by the mouse and box-select. All objects can be selected in the outliner, and are selected using circle select (C) and select-all. Meanwhile, the left mouse button moves the 3D cursor, but it does not work on manipulator widgets on any objects.
To replicate, in the default cube + light scene, right-click on the camera, or on the cube after selecting the light. However, I haven't been able to replicate this on any other computer.
Screenshot in which I've selected all the types of object I can: http://i.imgur.com/Y56iA.png
In Edit Mode, right-mouse select appears to be working correctly on vertices, but transformation handles still don't work.
I'm using 64-bit Windows 7 Home Premium Service Pack 1, with Python 2.71 installed (but may not be detected). I have an ATI Radeon HD 5700 series card and an Intel Core i5 CPU. I've attached the other system information detected by Blender in system-info.txt. I updated my graphics card drivers to the most recent drivers on the AMD site.
I've reinstalled Blender 2.63 several times in 64-bit and 32-bit, using both the installer and 7zip version. When uninstalling Blender, I've used CCleaner to remove remaining registry entries. I've also tried installing Blender outside of Program Files and running it as Administrator. This hasn't been successful.
Inside Blender, I've reverted to factory settings, and checked that the control settings are correct - the appropriate entries appear to all read 'select mouse' (shown in screenshot). If I change 'select mouse' to be a keyboard key (I used Q), the same problem seems to occur: I can only select lights and speakers.
Switching from right-mouse select to left-mouse select does not remove the problem: with that change, left-mouse select fails to work in object mode in the same way as before.
I've checked some previous versions of Blender. The problems do not occur in in 2.49b, 2.50 alpha 2 and 2.60a.
In 2.61 and 2.62, I have the same problems as in 2.63. (In all cases but 2.50, I'm using the 64-bit Windows installer).
I've googled this with as many strings as I can think of, and apparently a similar problem has happened to some Ubuntu users (example: http://blenderartists.org/forum/showthread.php?179540-Can-t-select-individual-objects-in-Ubuntu... ) but I can't find a Windows example. The Ubuntu users I've found fixed the problem with a graphics card driver update or an update of Ubuntu.