too many to pick but here are a few of mine
The Four Aces (London) - old reggae club in Dalston with a fearsome reputation that began diversifying mid-90s. I found myself invited to a Halloween party there in 98 and it just blew my mind. Upstairs was all strange goa trance and stuff but we hotfooted downstairs where there were endless corridors with people strung out along the ragged carpets (probably students and a few local crackheads) then there was a main room of sorts where people were going nuts to the filter house that was big at the time basement jaxx, sneak, MAW, armand van helden, daft punk, etienne de crecy etc. mindblowingly good. (Now flats, of course)
The Key (London) - the security weren't the ahem friendliest but if you could get past that (and them) it was a fantastic club with an illuminated floor that almost looked like a kid's dance mat with another room with chandeliers and mirrors and stuff. Saw many of the greats there, DJ Pierre, Greg Wilson, Rolando, Dixon. Hearing dubtribe do it now in full at the end of the night was something special. The last stand for the old King's Cross before the yuppies took over.
Amerik (Sète, Fr) - no longer there I hear but this was a beautiful open air beachside club opening out on to the rocks, with landscaped setting and water cascading down into rockpools. There was a live music venue in a Roman amphitheatre next door which I think has survived. Quite simply the best openair club I ever went to, even if it was only really us going hell for leather (this was 2006)
Sub Club (Glasgow) - reputedly the finest system in the UK and a great crowd too. all the best in the world played there - went up a few times to see pals and fitted in Larry Heard and Secret Sundaze amongst others (great warm up Telford and of course Harri & Dom).
still breaks my heart, I will never experience any of that again