(Note - it is possible for other applications to leave your system (windows, directx) in an unusable state. in this case, the fault lies with the other applications, not PJ64).
"Direct3D failed to initialize your HAL device. Make sure you have a properly configured 3D graphics card compatible with Direct3D 6.0" - Why won't the D3D graphics plugin initialise?
There are quite a few possible causes of this, so please read this section carefully before asking for help - this is a fairly common problem.
The first thing is to ask yourself "Do I have a hardware 3D accelerator?". If the answer is "no", you cannot use the Direct3D HAL, and you effictively won't be able to use Project64, so go no further*. If the answer if "not sure", find out from the people who made your computer, or look in the Windows control panel for your model and find out on the web is it has 3d capabilities. If the answer is "yes", we can probably get you going, so read on
Have you exceeded the capabilities of your hardware? The simplest thing that may work is to try changing your desktop colour depth to 16-bit (that's "High Colour", not 16 colours). Some cards can only render in 16-bit mode, while others have issues in higher depths that stop then running PJ64.
Now check you have the most recent drivers for your video card properly installed. This means downloading the newest drivers from your card manufacturer's homepage, uninstalling your current ones using Windows Add/Remove programs (there should be an entry in there for them) and then running the install program for your newly downloaded drivers. After installation is complete, reboot Windows if the software doesn't force you to anyway.
If you've done this and the plugin still won't initialise, reinstall DirectX and the drivers for your chipset. You get DirectX from Microsoft's site, and you get your chipset drivers from your motherboard manufacturer's site. Reboot Windows and try again.
Next thing to try - fiddle with your video card driver options. If there is a tweak utility available for your card, download it (try
www.tweakfiles.com) and use it. Relevant settings to edit are z-buffer depth, texture colour depth, and probably others depending on the card you have. If there is no tweak utility, look under Windows display properties (right click on desktop > Properties > Settings > Advanced). Your video card drivers may provide extra options on the screens there.
*You can technically run the D3D plugin using RGB emulation but the performance and quality will be dire even on the fastest of systems.