U will find:
Quarke for quake-good level builder but needs to be configured. However it is free, it does work and does not expect royalties.
Pakscape or Wally to develope your pakfiles.
Milkshape 3d to create your entities- Monsters, objects etc
It is not free ($29) but the demo will allow you to give it a go and it will provide your modelling needs. It is used by anyone who makes mods for quake, half-life etc
A bitmap editor although Wally should do.
I have found these to be easy to use once you overcome the truama of unfamiliality. Persevere cos it's well worth it.