I think the current color is okay because it stands out, and the other colors the remaining colors that aren't already used for some kind of weapon or armor or still pretty wacky.
If it had to change, I would vote for yellow. Yellow is kinda overloaded as it stands, but that also means it immediately jumps out at me when I'm playing... yellow things are all really good, and I'm going to look at all of them anyway.
To facilitate further discussion, here are the only colors used in DoomRL currently.
I'm not sure if there are any more that could be added.
Colors that are already used for armor/boots/weapons:
light gray (silver) used for pistol, steel boots
gray (dark gray) used for shotgun
blue (light blue) used for combat shotgun
white used for double shotgun
red (dark red, maroon) used for chaingun, red armor
brown (olive) used for rocket launcher
teal used for plasma rifle
purple used for bfg
yellow used for advanced weapons, upgraded weapons, "artifacts"
green (dark green) used for green armor, protective boots
navy (dark blue) used for blue armor, plasteel boots
light green (lime) currently used for unique stuff
Unused colors:
cyan (aqua) (same color as magazine mod)
magenta (fuchsia) (same color as accuracy mod)
light red (same color as small med-pack)
black (used for...background)
The colors appear a little different on the board than in game, so I included other items of the same color so you know what the color looks like in game.