The first top clan I believe was [=CC=] (Carnage Cowboys). Silkk/botch played WFA but there may have been others. In the early days of Q2WF you could win on points alone. I plan to post a really old demo between [=CC=] and HO! (Thundercats) where [=CC=] won in the 3rd round by playing all defense.
After them, <^> Legacy was unbeaten for a really long time. The demo I posted below is, from my understanding, the last match they played in and the only match the lost. SnowCrash and Suicidal quit after that game. Other than Suicidal, Hollow also played in Legacy. I'm not sure if anyone else went to WFA.
After Legacy, =PCI= (Population Control Incorporated) was the top clan. =PCI= played in WFA for a brief while but got beat pretty badly by {IS} and quit. Some of their players ended up going to HLM after they disbanded like Mudsloth.
After =PCI=, [SR] was the top clan. I believe in their entire history they lost a single map... to =PCI=. I will post that demo shortly. I don't know if anyone that was in [SR] ended up playing WFA or not.
Once [SR] retired things were a little more interesting. [HLM] (Hot Little Monkey), :RR: (Rough Riders), +]F[+ (Fate), :[Z]: (Can't remember the name?), and ]$[ (Unfadable) were all top teams at one point or another. Q2WF died off in the late spring/early summer of 2000 when WFA started having clan play. :RR: had a lot of players that ended up in .x., MACHINE, and ultimately the WFA version :RR:. [HLM] basically kept the same roster when moving to WFA and stuck around for a while. ]$[ obviously went to WFA as well.
Other decent clans in Q2WF that went to WFA...
[GQF] (Global Quake Forces)
]II[ (Invincible Invisibles) (Most dominant Euro clan by far)
{IS} (Infernal Seraphs)
MACHINE
[T] (Tribe) + =SFT= (Special Forces Team) =TF= (Tribal Forces)
=SLJ= (Samuel L. Jackson)
There may be others...