This is all opinionated but a survey could be created to pick the real winners and losers here

My most hated
1. Piranas
2. Roots
3. Extended Uppers
4. Pussycats

My most hated:
1. Jungo
2. Roots
3. Pussycats
4. Piranas
5. Junkz

my guess on most used:
1. Jungo
2. All Stars
3. Piranas
4. Junkz
5. Freaks

(this is elo based mostly)

most underplayed - good clans but without much recognition:
1. FPC
2. Sentinel
3. Berzerk
4. Vortex
5. Sakrohm

My Most Hated

1. Morphun
2. Ambre
3. All Stars
4. Ulu Watu
5. Pussy Cats

Underrated


1. Skeelz
2. Fang Pi
3. Freaks
4.Geist
5. Jungo

My list is NOT personal preference but actually is a guess of general preference.

Most used (Elo) (recent)
Rescue
Montana
Roots (if Gertjan and Tuck aren't banned)
Skeels (if Greem isn't banned)
Frozn (since Stompah was introduced)
Leader missions clan

Most Used (DT)
1. Montana
2. Uppers
3. Junkz
4. Vortex
5. Newblood
6. Ld mission clans

Most hated (genaral)
1.Piranas
( I like Piranas but its genuinely the most hated clan by players. Why?.. well lets see... Kalindra, Beeboy, Troompah, Saki all of them manage to avoid the weekly elo ban once or twice a month. But Lizbeth always fails to manage that.)
(Ulrich has the same stats as Jeena and yet he was banned by players and eventually by staff)
(Raeth and Petra have same stats yet Raeth has been banned more than Petra)
2.Roots (So many bans, but hated more by staff than players themselves)
3.GHEIST (So many bans)
4.Bangers (hated by card makers just look at their abilities: there's no variation)
5.Berzerk (hated by creators of the game, they have inherited the worst bonus a clan could have, Jungo can stack their life bonus, they don't have a max. Berzerk have a min of 2, making them unable to 2HKO like Junta or FPC.)

Underrated. (general)
Ulu Watu
FPC
Sakrohm
Junta

Rarely Used (Ld missions do not count)
Ulu Watu
FPC
Sakrohm
PC
Freaks
Sentinel
GHEIST
Bangers

My Most used:
La Junta
Sakrohm
Uppers
Montana

My most hated:
Nightmare
Piranas
Roots

Rarely Used:
Berzerk
Freaks
Bangers
Sentinel
Frozn
GHEIST
Pussycats

Create a Survey I would be really interested to hear some results!

I pick which clan(s) I play at random to keep things from getting too monotonous (I use a special die for that). Though I find that some clans don't work as well together like Freaks-Roots (never head much luck with that combo). So it's a bit trickier with me for answering some of these questions. Though Kolos alone has given me a ton of headaches since he's can be easily abused (though it is so satisfying to take down anyone who tries the Kolos Trick.)