The most obvious one, and one I'd expect to have just about everyone say: The Galactica. I loved her in the first series, and loved her in the re-imagining. The Pegasus was prettier and sleeker, but never had the character of Galactica.
The HMS Nike, from David Weber's 'For the Honour of the Queen'. She was a gallant ship, pounded into scrap through battle, and her name placed on the List of ships whose names will never die.
The HMS Surprise.