None of the released players are big surprises, with only Southall involved in recent weeks.
The 37-year-old played his 375th and final game for the Gills when he came on as a substitute in the play-off semi-final second leg against Rochdale at Priestfield.
He was dropped for the final against Shrewsbury at Wembley in favour of Adam Miller.
Striker Mulligan was widely expected to leave last summer, but opted to stay at Priestfield for another season.
Former captain Crofts, who was born in Medway, skippered the side at the start of the season but fell out of favour and ended the season with Blue Square Premier side Wrexham.
Clohessy was brought to the club by former boss Ronnie Jepson but failed to make it into his successor Mark Stimson's plans, and ended the campaign at Salisbury.
Howard made just two appearances for the club, while first year pros Kiely and Thomas never featured.
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