I Recently read an article in my local newspaper regarding the Beagle, According to the article she is somewhere in Paglesham.(essex England)
I live quite close to Paglesham and know the place fairly well, it has a lot of little muddy creeks all over it (mostly leading into the river crouch) and each of these creeks seems to have one or two old barges/hulks/wooden pontoons laid up in them (all very rotten and probably dating back to the the last war.) according to a friend who keeps his boat on the river crouch the beagle is among these and was used as a hulk for some time before becoming too far gone for use, since then she has disappeared into the mud and obscurity.
I hope they find her as she is far to historically important to be left to moulder.
I watched a program a few months back about the possible discovery of the Beagle. It is indeed supposed to be in the mud in Paglesham, Essex.
When the ship was finished as a sea going vessel she was moored in the river Crouch as a base for Customs men. I wish I could recall more but I do remember that ships timbers matching those of the Beagle were found in the fabric of a nearby boat builders.
I hope these links are useful; http://observer.guardian.co.uk/uk_news/story/0,6903,1148523,00.html