The Films
Both films had incredible movies to be honest. Whilst today I think the Ghostbusters ones hold up better, the TMNT ones are a HUGE part of my childhood, and the nostalgia still makes them awesome films, including the third one. Haven't seen all of the CGI one, but it seemed alright what I saw of it.
The Original Cartoons
Turtles win this one no doubt. Easily one of the greatest cartoon series of all time, and pretty much my obsession for the first few years of my life. The GB cartoon was also cool, but I seem to remember there being a billion more Turtles cartoons, and the GB's just couldn't touch that. Plus the Turtles had a much bigger cast of characters/allies/enemies etc, which made for more varied episodes.
The Reboot Cartoons
Haven't seen too much of either to be honest. Didn't really like Extreme Ghostbusters (that's the GB reboot in question right?), and I didn't get to see many episodes of TMNT, however, the episodes I did see were pretty good, and pretty loyal to the more ninja-esque aspects of the Turtles. The Turtles Forever animated movie was incredible though, whilst the Extreme meet the Real Ghostbusters was kinda crap.
The Toys
I'd have to go with Turtles again. Whilst GB toys were cool, there wasn't really much to go for compared to Turtles. Turtles had EVERYTHING! No doubt the GB house was an awesome playset (ditto the slime complaints) and the photon pack/ghost trap were good fun back in the day. The Turtles though... wow... the sewer lair, the blimp, the Technodrome, the fugures and a billion different versions, such as movie stars, horror stars, space, surf, ninjas, movies... holy shit.
The videogames
Can't really comment here. Only game I've played was this one:
The children
I'd imagine the Ghostbusters children would be better looking, and how would the Turles ever have kids anyway? I doubt April O'Neil would put up for them. However, if the Turtles could have children, they'd end up looking like Franklin, so the Turtles get this one.
In conclusion, the Turtles get my vote. The Ghostbusters were awesome back in the day, but the TMNT pretty much WAS my life throughout my childhood. I miss such innocent times...