when Squall is being tortured by Seifer at the D-District Prison, Seifer mentions that Galbadia will destroy Garden, and "after that, the SeeD Hunt will begin", in retaliation for SeeD's botched assassination attempt on Edea.
This is eerily similar to the Jedi Purge in Episode III, where following Mace Windu's botched attempt to arrest Palpatine following his unmasking as Darth Sidious, Palpatine intiates 'Order 66', declaring the Jedi as enemies of state, and causing Jedi to be hunted down and exterminated.
Unlike in FFVIII though, where Seifer's threat never actually came to fruition, apart from the missile attack on Trabia Garden, the Jedi Purge actually succeeded, bringing the Order to practical extinction before Luke rebuilds it twenty or so years later.
Although FFVIII predates SW Episode III by a good six to seven years, the Jedi Purge had been referred to long before then though, way back in 1977 at the start of the original trilogy. So the reference still stands.