Bench: I usually just work up towards a five, triple or single (once a week). I used Smolov Jr to break my previous plateau which worked pretty well. I gained weight while I was on that routine though, so I'm not entirely sure where to attribute the success to.
Squats: All I've done is 5x5 (same weight every set) up to this point. Started squatting about 1.5 years in to lifting - really silly.
Deadlift: I'll work towards a working five, triple or single once a week or once every two weeks.
Also do OHP 5x5 (same weight every set) once a week.
I usually pair two of the above lifts together (whatever I feel like doing) and do them in any one session.
Run and swim
Definitely agree on the squatting. Will look into what the guys above have recommended. If you have your own suggestion, that'd be appreciated!