The best CTF mod was the original Expert CTF. It came out before Threewave CTF and used a all of Quake1's ingame models. Basically, one team had a silver key for a flag and the other team had a red key for the flag. There were 4 or 5 runes and they were the same purple runes from the single player game. There was a grappling hook and it was made up of the Vore's (spider thing) purple projectile attack. The best part was it used the original levels from the game as CTF levels. Since these levels were not created for CTF, each base was entirely unique and the levels had a very crazy feel to it.
IE, one of the best original Quake1 maps for CTF was the Elder God Shrine (E3M4 I believe). One team had their base in the graveyard that you could get to from underwater only and one team had their base at the end of a floor that moved when people ran across it to reveal a huge lava trap. This bases were, by design, equally unfair, which made the base attacks extremely unique and fun. Another fun aspect of the map is that it had something like 3 quads.
<3 Quake1