Taking the risk of reviving an old thread, I arrived here looking for something else completely but got drawn into the replies. A few London candidates for the worst:
London Bridge P6, as previously mentioned. Completely inadequate for the number of people who use it, cramped layout, simply getting a cleaner in for 10 minutes must be almost impossible for large parts of the day. Smells horrendous.
Seven Sisters (BR northbound platform) - tough clientele, in a difficult area, on a platform that sees trains taking people home to other difficult areas. Toilet frequently blocked, floor usually covered in puddles. Also located down the back out of sight of most pax/staff (who aren't inclined to deal with trouble in any case) so a lot of misbehaviour of various sorts takes places around/inside it. Very rarely actually closed, though, credit where it's due.
Willesden Junction (NB DC platform) - constantly vandalised, smell terrible, very poorly lit with those drug-deterrent blue lights, not unusual to find human 'deposits' all over the floor. Slightly better cleaning/maintenance care with London Overground than in Silverlink days, but with some of the users it gets there's only so much you can do.
It should be said that even the worst toilets I come across on NR aren't a patch on many bus station/local authority run toilets I've had to use.