I've noticed that darkplaces clears the screen each frame which may not be necessary. Normally the color buffer only needs to be cleared if there is some chance that the entire screen will not be written to. Since most correct non-leaky maps should always paint the entire screen not clearing the color buffer each frame should not be a problem.
I've tried removing the GL_COLOR_BUFFER_BIT flag from all calls to GL_Clear() and qglClear() other than the one time call in GL_Init(). The rendering is not noticeably changed other than the fact that leaks in leaky maps are no longer black, but just not painted. Also the Alien Trap logo was not removed perfectly.