Especially on my Strat if the cable gets even slightly bumped it generates crackles, the cable is typically routed up behind the strap/strap button which helps but isn't the ultimate answer.

I have a soundcraft jack in guitar body and Neutrik jacks on the cable so that shouldn't be the problem, are there any other tricks to preventing crackle?

Take a piece of 1000 or 1200 grade sandpaper and give the contacts inside the receptacle a light sanding. Also check that the nut holding the plug isn't perhaps a little loose, If it is tighten it.
And lastly make double sure that your soldering on the wiring isn't perhaps a bit dodgy.
One more thing,,,,,
Sometimes you may just need to bend the contact that touches the tip of the jack plug a little further in.

Does it crackle with all amps or just one?

Sounds like an earthing problem somewhere then,,you'll probably need to check all the wiring carefully.
Is the crackling like static?

Skylark wrote: Thanks Costa, all checked bar the sanding, jacks are all fresh though. I've tried the bending of the contact in the past, didn't seem to overly help. Is this crackling something I need to live with, would have thought using the best quality connectors would sort it out?

Remember, the ground contact in your jack, is the inner sleeve itself. As per Costa's advice, roll a piece of sandpaper so it can just slide into the jack, and rotate it around and around, thus cleaning the inner sleeve. Slight corrosion in there is (in my experience) the most common cause of crackles and bad contact.

If all of the remedies suggested do not work, REPLACE THE JACK. Even Switchcraft jacks need replacing. ?

Have you tried another cable? Have you tried the cable on someone else's rig? Both quick checks to see if the problem is in the cable or the sockets on the guitar/amp.

I have recently stripped a cable to sort out an issue with a cable only to find that the wires inside the cable are damaged. I found a kink in the inner core and places where the shielding was not properly surrounding the core. I have also found cables where there is more resistance than normal which causes signal loss. So it may not be the connectors but the cable itself.