We have had similar problems here in the past, below is a document I created for internal use if it happened while I am not here.
Forced snapshoot removal.
Step 1 (backup, or can use anther method you are confident of restoring from)
Turn off machine
Make a backup of machine, this can be done with following command from a putty session (alter path)
cp -r /vmfs/volumes/Raid5-4/ex/ /vmfs/volumes/Raid5-4/exnew*
This new machine can then be registered by browsing to vmx file, right click, register virtual machine, when turning on do as recommended and create new ID.
Step 2 (the easy way, most people report this to work, but not always...)
Create new snapshot on machine
Try to apply all snapshots (delete all) in VC
Step 3 (using the command line)
Run following from a putty session (alter path to correct VMX)
vmware-cmd vmfs/volume/Raid5-4/ex/ex.vmx removesnapshots
This should remove all snapshots
This takes can take ALONG time, but do not presume it doing nothing, and do not stop once started. You can check what it's doing using WINscp (or anther method of checking if file size is changing, I do not trust browsing the data stores) Keep refreshing and you should see files sizes altering).
Alternative step (some report below works, but did not for me)
As an alternative to above people with similar problems have reported fixing it by using VMware tools to clone the disk, but this did not work for me.
vmkfstools -i /vmfs/volumes/Raid5-4/newex/ex_2.vmdk /vmfs/volumes/Raid5-4/newex/ex_2new.vmdk
Then re-point disk to new.vmdk (NOTE once you have re-pointed disk to new one it's VERY tricky to point back to snapshooted version, only do this if have a good backup!
Other useful command if a host stops responding, or fails to complete a command due to file in use type error (but be carful not to do this while snapshots are being removed):-
service mgmt-vmware restart
Also consider consequences if bring up a back up machine that you may decide not to keep, e.g. I disabled mailsweeper delivery service before started.
