Arcana Unearthed has an interesting system for teleport, which looks like it might limit it a little bit, without crippling things. It would also give a built-in way to adjust things -- e.g., certain areas add to the DC to teleport in, some building techniques (blood of gorgons, or just the right feng shui) increase the DC, items etc. Other areas or items
PS: I'm Talon5's GM; the Underdark limits I took from Vault of the Drow, which seemed appropriate to me, since I'm running a game in Greyhawk. Plus, there was this Elder God/Thing Man Was Not Meant To Know rising in the deep, gathering Its power to Itself, and generally mucking things up. I blame Piratecat.
Myself, I think unlimited, very reliable teleport tends to be either bland, requires common & relatively easy countermeasures, or leads to a setting like RangerWickett described (or one like Brust's Dragaera) -- but I suspect some people would find such a setting too different to be interesting for long.
Note the handwaving which Star Trek writers have gone through trying to limit transporters -- range limits, not through shields (except when they can), not through "ion storms" (execpt when they can), etc. Other SF universes go through similar contortions to limit their FTL, to achieve particular results (e.g., Traveller's 100D jump limit, 2300 AD's 7-odd lightyear limit, MechWarrior's JumpPoints, the FTL systems in Weber's Honor Harrington novels, the limits of the goa'uld's Stargates, etc.). All of those settings would be much less interesting if the teleport effects didn't have some limitations.
So I prefer teleport have some flavorful limitations.
Making teleport difficult, but with interesting ways of easing the difficulty is one fairly useful way of adding flavor and complications. GURPS' Teleport spell, for example, comes with hefty costs & skill penalties, such that while long distance teleport of multiple people is possible, it is fairly difficult (or requires Beacons, which makes it more akin to the previously mentioned Town Portals & the like).
Single person-only teleport is another interesting idea, but it would probably just lead to all the non-teleporters climbing into
bags of holding or
portable holes for transit home.
Teleport with side effects could be fun -- the dispel magic effect (leading to teleport as a form of attack -- grab someone & try to teleport them into an ambush, simultaneously stripping away magical defenses), teleporters are stunned or nauseated or otherwise inconvenienced (hey, tearing up reality can be unpleasant), teleport causing some sort of advance warning at the destination (e.g., a rainbow shimmer grows at the destination several rounds or minutes before you arrive -- either teleporting isn't actually instantaneous, or people at your destination will have hints that you're coming before you actually leave -- take
that, cause and effect); a complete & working system of measure, countermeasure, and maybe counter-countermeasure (which D&D doesn't really quite have -- there's dimensional lock, but that's significantly more difficult than teleport); etc. There are tons of possibilities.