Like many I like usually use a Crown of Thorns. Immobilises queen on comb and gives me time to check pens and have scissors handy before marking and sometimes you get lucky and a wing protrudes through. Otherwise I mark and clip later. Clipping I usually have scissors in one hand and pin queen to comb with thumb and forefinger and clip.
However, I've been playing around with these push and turn cages from Thornes. The beauty of these is you cannot crush the queen as they have a stop to prevent you doing that. You do need to pick up queen to pout her in (remarkably easy when you realise how tough they actually are, just use their wings as your gripping point) , but the other advantage is you get rid of the rest of the bees that can be a nuisance when you are trying to mark your queen in CofT.