I only used to use plain water in my camelbak and therefore never used to clean it.
I recently went on a cycling challenge in China and thought I needed some powered formula stuff to supplement me on my long rides.
When I came back to the UK I chucked the camelbak in the corner of the garage and you have guessed it - I didn't clean it out; it was still half full of liquid. i used bottles and another camelbak (with water) for a couple of months. When I went back to the first one it was all moldy with black sooty type stuff. Nearly chucked up first time I tried to use it and swigged the contents!
Even after repeated flushing with clean water the black stuff is still stuck in the tube.
How do I clean it?
Use warm/hot soapy water to remove as much of the mold as you can, then rinse it out. Then add some baby bottle sterilizing solution to the bag and ensure you thoroughly flush it through the tube valve etc. Sterilizing solution is available from pharmacies and supermarkets the brand name is "milton" but there are cheaper equivalents. You can either buy tablets or a concentrated liquid (I would probably make it up stronger than the instructions describe - e.g. 1 tablet in a 2L bag). Leave it overnight, giving it a gentle shake every so often, then drain out, and flush with fresh sterilising solution. Rinse with clean water and either dry thoroughly (assuming all signs of mold have gone) or store in the freezer until needed (mold spores are incredibly hardy - and even with the sterilising solution you may not have killed them all, so you need to stop it recolonising).
You could use houshold bleach rather than milton, but in my experience its harder to rinse the taste off stuff.
One word of warning - don't leave your bag anywhere children might get to it whilst soaking - a friend of mine did recently, fortunately very little was consumed.
cotton wool and some cotton or fishing line!! down the tube to pull all the black crap out!!
I've got one of the long thin Camelback cleaning brushes, stupid money for what it is, but makes the job a piece of cake. You could probably get a similar brush from a homebrew wine shop.
If it's really bad you may need some mechanical cleaning as well as Milton soaking. I managed to do it by inserting a not too tight plug of cotton wool in tube at mouth end. Then use a straightened wire clothes hanger to push it up into the bladder. Easy then to empty out of the fill port. I recommend freezer storage. I now keep mine in zip lock bags to keep the tube under control, much less hassle then in freezer.