Lunge powers like the viper stealthers, the ground pound that bear manamals use, super strength leaps and basically any power that you yourself can put "Nailed to the ground" advantage point in turn off all travels powers.
I don't recall if they could shut off teleport but at some point or other teleport speed was severely nerfed and you can be damaged while phased... although I haven't used it in quite sometime so perhaps they changed that.
SAM sites and Flak cannons were also incredibly deadly to super jump and flight users.
(Tough) Enemies could and I think still do detect you while your teleporting. All teleport in CO does is let you pass through npcs and player characters and makes you invisible with a high stealth rating. But anyone with an extremely high detection can still spot you and shoot you, even while teleporting. I ran an experiment once when the game still had radar mods, and with three of them and even a mediocre intelligence a teleporter could be spotted and shot down. I even had an alt build specifically for countering that back in the day.
SAM sites and flak cannons used to be a problem to, though I notice the damage had been dropped very sharply recently, a shame really. They could have easily buffed those to give vehicle users something to worry about instead of nerfing vehicles to general uselessness like they had recently. Edit: By quite litterally nerfing the only good things vehicles could use and ignoring the fact that every other mod and weapon not being used were not because they didn't even work.
Another Edit: And, the above in the top paragraph is the reason I didn't care for teleport in CO. Besides reactivating it constantly, it mechanically was not really teleporting anymore once I learned how it worked. I sometimes take teleport in CO even today but, I admit, I liked teleport in city of heroes alot more because it was an actual teleport. The moment you knew how to use it, it was actually a very flexible and easy to use ability. And people even came up with binds to make it more usable. CO's teleport is a generic dumbed down stealth flight.