Are there any pagan temples that have been converted to mosques or churches in Europe/Middle East?

The Kaaba.

the Pantheon in Rome was a pagan temple but is now a catholic church

Several churches in various locations in Europe and the British Isles were built over pagan locations, such as the Cathedral of St John of Beverley in Beverley, Yorkshire, England. There is a Zoroastrian Fire Temple in Armenia that was converted to the Armenian Orthodox Church. Hagia Sophia in Constantinople became a mosque, although now it is a major museum in Istanbul.
There are a couple former Hindu temples in India and Pakistan that were made into mosques–one was in the news a couple years ago as Hindus were demonstrating for its return.

The Dome of the Rock is not a Roman temple. It was built as a mosque.
One example of a Greek temple converted to a church is the cathedral of Syracuse in Sicily. Interestingly, the transformation involved turning it inside out, so to speak – the spaces between the outside pillars had to be walled up and the inside walls had to be pierced with arches.

There’s a lot of urban legend and rumor about churches in Europe being built over pagan temples, but I’ve not seen evidence for most of the claims, and in some cases the claims have been outright false. Kildare, however, is one example where a pagan shrine was converted into a shrine for a catholic saint f the same name (Brigid)