Because the video plugin has so many options, I have divided the topic by the tab of the plugin config. dialogue. To access all tabs, you must uncheck the Hide Advance Settings checkbox.

Below all the tabs are three buttons, OK, Cancel and Apply. Hopefully the first two are self-explanatory - cancel closes discarding changes, OK closes keeping changes (but they aren't acutally written to registry (disk) until you close Project64. The Apply button (new in v1.4) is to allow you to see the effects of changes to graphics configuration in real time, while a game is running (only for controls which take effect instantly, which is most of them in 1.4; this is detailed with every control), without the awkwardness of having to go back to the dialogue every time. This button does not save changes to the registry - saving to the registry is done on application exit. Therefore its a good idea to restart Project64 once after making a lot of changes that you want to keep, just in case anything crashes.

Troubleshooting graphics problems

The first thing to understand is what level of graphics quality to expect. Games marked compatible should look generally good and not have any flaws serious enough to stop you playing the game. The screenshots you see on the internet should give you some idea what to expect. Perfection is not realistic to expect, regardless of how good a system you have, because the emulation isn't perfect, and nor are the APIs used (and, interestingly... nor are the games themselves).

Before you ask for help, please take yourself through the following questions:

1. Is the problem a limitation of your video hardware? Do you meet the recommended specification? Remember that different games and different parts of games use different hardware features - only the recommended or better hardware can display everything the plugin is capable of. If you have poorer hardware, you may be able to get better results from older versions of the video plugin, which use less complex effects. You can see whether any problem is a limitation of your system or a bug in the emulator by selecting Reference Rasterizer in the video plugin options and comparing the result to normal Direct3D HAL - if the problems dissappears in Reference Rasterizer, it's your fault, if it doesn't, it's the emulator's fault. Basically.
2. Does the problem lie with your video hardware drivers or driver configuration? Try newer drivers (or sometimes older drivers help). Be wary of tweak utilties and beta/leaked drivers. Make sure you uninstall drivers properly when changing them. For example, the ATI Radeon hardware is capable of drawing everything that PJ64 asks, but many of ATI's drivers aren't, and your system is only as strong as the weakest 'link in the chain'.
3. Is it a problem with your video plugin configuration? Have you changed anything from the defaults?
4. Is there an instruction you have to follow to configure the emulator specifically for that ROM? Check the ROM Browser Notes. e.g. Aidyn Chronicles needs Display List Culling disabled.
5. Is the problem a known game specific issue? Check the ROM Browser Notes e.g. the Conker's Bad Fur Day has a problem with the pause screen. You can't do anything about known issues, except look out for an updated or better emulator.
6. Is the game using a framebuffer effect at that particular point? Try all the framebuffer options to find out. The framebuffer can be used for all sorts of things that are not obvious to the user e.g. one of the gun scopes in CBFD multiplayer.
7. Is the problem a known general plugin issue? e.g. the near clipping plane problem, you may only notice this in Extreme-G but its a general limitation of the API that effects all games.

Remember graphics problems are not necessarily the fault of the video plugin, they could also, though it less usual, be caused by faults in the core or RSP of the emulator you are using. If you are using Jabo's plugin with the core of another emulator, try with the complete Project64 package first.