When you try to redeploy Pipeline Components BizTalk locks the dlls under C:\Program Files\Microsoft BizTalk 2006\Pipeline Components. They are locked by the BizTalk Host Instance that used them. To update a Pipeline Component one has to stop the Host Instance, redeploy and then start the Host Instance.
UPDATE: Thanks to Th Almeida who pointed me to this: Pipeline Components are locked by the host that is using the pipeline not by the standard host. I did my pipeline deployment test with a dynamic port and NTLM authentication which means that the pipeline gets executed under the standard host. (I have already corrected this in the abouve blog statement to prohibit confusion)