TOS defined visual effects for the 60's, imagining things on a scale hitherto unseen in science fiction, be it on television or at the movies.
TMP did largely the same thing for the 1970's movie audience, reimagining the Star Trek universe on a scale, and in a way that was relevant both to the new medium of the franchise, and the moviegoing audiences who were quickly getting used to whizzbang space effects thanks to Star Wars. It's a shame Star Trek II and III couldn't maintain the same level of quality in their visual effects (and yes, I know this was caused by them having much, much lower budgets than TMP enjoyed). Fortunately, Star Trek VI allowed the TOS movies to go out on an effects high. As has been said before, the final battle between Chang's BOP and the NCC-1701-A was extremely well realised on the big screen, as was the Praxis shockwave.
TNG's effects were initially rather weak, particularly in the first and second seasons, but anything from Season 3 onwards was pretty much state of the art for the time, and by the final few seasons, TNG was regularly putting out eye popping visuals by the standards of early 90s television. A standout for me is the Enterprise-D navigating the asteroid canyon in "Pegasus".
However, the defining moment for (modern) Trek effects for me was the transition of Voyager from a traditional miniature based, stock footage kind of show to a production fully dependant on CGI from Foundation Imaging (ex-B5) for its effects, barring the occasional reuse of a stock model shot - it was done so seamlessly that most viewers probably didn't even notice the difference.
The new technology allowed them to push the envelope in television FX (the resulting effects were far more convincing than Babylon 5 ever was, probably down to Voyager having almost twice the budget to play with), and to finally show Voyager taking some damage - something that would've been practically impossible if they'd continued to rely on miniatures and motion control photography. CGI also made the Dominion war battles in DS9 possible.... they would have been an absolute nightmare to plan and choreograph using motion control and miniatures.