Pipe cleaners are your friend
Remember pipe cleaners? As a kid I didn't make the connection between smoking a pipe and these incredible craft items that I used to make sheep and cows out of. However now I realise that they're great for getting into all the fiddly bits of the pipe. After each smoke I give the pipes a good clean with some of these. They're also very cheap. Don't be tempted to tie a load together and push them down your hose though, remember they're essentially wires and if the sharp bits come free you could end up damaging the hose. Only use on the hard bits of the pipe, and carefully.
Use a fluid
Check out our orange cleaning solution : http://www.theshishashop.com/magic-orange-cleaner-hookah-shisha-cleaning-solution-p-661
This is ideal for cleaning the jar, clay bowls and stem. Also, some washable hoses can be cleaned with this, but check first.
Simple one this. After each smoke and assuming you have a washable hose, run hot water through it. Then, hold each end of the hose and shake the water about a bit before letting it out then blowing through the hose. If you do this regularly then you won't let anything build up at all so a big scrub and clean won't be necessary.
Resist putting your pipe through the dishwasher. Trust me, from bitter experience this isn't a great thing to do at all...