I'm a big fan of Star Trek, and answering this question is kind of hard. I've seen all the series to their end, save Enterprise, which I haven't seen the last season.
Which is why I think I must tell you that you shouldn't leave out the animated series :-p ... I'm positive I've seen the Gorn in one of those episodes, don't remember which one though. (edit - looked it up, it was "The Time Trap")
But when it comes to my favorite series, I guess I'm going to have to go with Deep Space Nine. Looking back on my marathon star trek watching day, I seem to remember and enjoy that series the most. A lot of people didn't like the prophets storyline, but it wasn't the only thing to like about the series. Gol Ducat was probably the best bad guy ever created for the universe. Odo and Kira was so cute as to be a tear jerker (and I could relate with Odo, loving someone from afar like that.) Add to that, surprise cameos from The Next Generation, and the devious, money-minded Quark, and I have to say it gets my vote as my favorite.
But thats not to say that I don't absolutely love everything else Star Trek. It's just my favorite
On a bit of a side note, I'm not advertising or anything but if there are any trekkers out there that would love to see all the series, but don't want to pay a god awful amount of money for all the dvds, Netflix has all the Star Trek series currently. I've been picking and piecing my favorite episodes from all the series's for a few months now.