In 2005, Colin Percival discovered and presented a security flaw with then newly-introduced hyper-threading on Intel Pentium 4 processors, which, in summary, says (from abstract):
...shared access to memory caches provides not only an easily used high bandwidth covert channel between threads, but also permits a malicious thread (operating, in theory, with limited privileges) to monitor the execution of another thread, allowing in many cases for theft of cryptographic keys.
In 2006, (as a result of the discovery?) Intel removed hyper-threading from Core microarchitecture, introduced in the same year.
In 2008, Intel re-introduced hyper-threading in the new Nehalem microarchitecture.
Although it's not entirely clear from the quoted sources whether the removal of hyper-threading from Core and re-introduction in Nehalem was in order to fix the issue, does anybody know whether and/or how Intel eventually fixed the issue?