I recall three truly memorable mods:
Cujo – mod for the standard single player experience. adds op attack dog (with custom skin) as AI co-op.
ReaperBot – great back story here which lead to Unreal Engine. is an AI opponent for offline multiplay.
Requiem – Quake World mod which introduced new maps / skins / weapons (with best grappling hook mod)
added extra mention of the Quake chess mod too!