Several problems...

[Zorander]

When I try to run Castlevania 2: Legacy of Darkness, all I get is a blank screen. Just black, no sound, no nothing. It says, in the ROM listing that it's Compatible. I'm running an AMD Duron 1.0 GHz, 256 MB PC133 SDRAM, GeForce 2 MX400, Project64 v1.4, Jabo D3D7 1.4 . Any ideas? Or have I completely missed something, which is entirely possible, knowing me...

Also, GoodN64 doesn't seem to be working properly. Again, it's probably something I've completely missed...but it keeps listing several ROMS that I used to have, but deleted, and I D/L'd a Castlevania 2, and it doesn't list it at all (which could mean that it's a bad copy...) Any help with either of these problems would be greatly appreciated...

[Pro]

Try refreshing the rom list to see your current games ( File->Refresh).

[Zorander]

No, Project64 lists the ROMs fine. I did, and it shows up. But GoodN64 keeps listing several ROMs that I no longer have anywhere on my hard drive, and it doesn't list the new one that I downloaded (which was named "Castlevania - Legacy of Darkness (U) [!].v64"). I'm not sure what's wrong with GoodN64, especially because it still lists two ROMs which I deleted, even if I completely delete the N64Have.txt, N64Miss.txt, etc... I tried re-installing it, and it still listed them.

[Doomulation]

Probably a bad rom. Use the rename option with GoodN64. All the roms it recognize, it puts in a sub-folder "N64Ren". If that rom isn't there, then GoodN64 doesn't recognize it.
And if it doesn't and it doesn't work, then you should try to get another copy of that rom.