FYI, microphonics are something else: either the valves themselves produce it, sometimes popping noises due to the elements inside not being temperature-stable (bad manufacture, loose plates and heaters, etc), sometimes an unwanted whistle (not heard in the speakers), and feedback from the outside world.
Just tap the low-signal valves gently with the tip if your fingernail to hear what it is.
Crackling noises can, as Jez says, be caused by bad contacts. I like to replace the offending valve sockets with new staetite ones, when they are too oxidized.
Otherwise I use ISP-dipped toothpicks to clean the contacts within the sockets (a few rotations should be enough).
Also look for any dry solder joints if it's a PCB-mounted socket.