I have just install doom3 in my neo folder using scons (ubuntu 11.04). I typed ./doom.x86 and I got the following message.

  DOOM 1.3.1.1304-debug linux-x86 Nov 24 2011     00:27:04
  found interface lo - loopback
  found interface eth0 - 10.0.0.19/255.255.255.0
  no 'base' directory in exe path /home/kun  /doom3.gpl/neo, skipping
  WARNING: using hardcoded default base path
  ------ Initializing File System ------
  Current search path:
  /home/kun/.doom3/base
  /usr/local/games/doom3/base
  game DLL: 0x0 in pak: 0x0
  Addon pk4s:
  file system initialized.
  --------------------------------------
  Unknown command 'vid_restart'
  idRenderSystem::Shutdown()
  Sys_Error: Couldn't load default.cfg