To answer the question rules-as-written:
Wherever the DM thinks appropriate. There appears to be no answer beyond that (especially nothing as specific as a table of default destinations) using official 3.5e materials - 3PP d20 material or earlier editions may be another matter.
For a more useful answer, we need to go beyond rules-as-written (which after all is the whole point of having a DM in the first place.) The best answer therefore depends on the style of game being played, of which there's infinite variation but here's a few ideas:
The narrative answer:
Wherever adds a good story twist, which probably means a populated area with NPCs to interact with. If it's the PCs first visit to that plane, a large city would probably be a good way to introduce them to the plane, as well as providing a useful home base. On the other hand, a small settlement would provide for more intimate interaction with local NPCs and lead to easier story hooks.
The conjectural cosmological physics answer:
The 3.5e Planar Handbook (p151) mentions planar breaches between planes, where the dividing line between two planes has worn thin. It follows that this would be a likely entry point to another plane, as the barrier between the two would provide the least resistance at these points. Planar material could be flowing in or out of this breach depending on the relative density of the planes concerned.
The Hollywood movie answer:
As mentioned in the opening question, there may well be a specific location on the destination plane that is related somehow to the point of origin of the travelers. Travelers from the plane of water may arrive in the middle of a lake or ocean, for example, while those coming from the plane of fire may arrive in a volcanic area.
To the best of my knowledge, there's no definitive list of these, and in many cases it's necessary to tweak the idea to something that would be appropriate on the destination plane - arrival from Mechanus may seem difficult to do if the destination doesn't have clockwork, but a ring of standing stones shaped like cogs feels like a good fit.
The random chance answer:
The DM grabs whatever maps or charts they have of the destination plane (sketching something out if necessary), makes up a grid reference scheme if needed, and rolls dice. Having a few easily adaptable generic maps at hand (with some locations that can easily be tailored to any plane) can be useful here. Tables would work equally well if preferred.
The murderhobo answer:
The PCs arrive at the entrance to the lair of planar monsters that need to be killed, because... they're not currently dead enough, and they have valuable stuff to take.
The "Teach them a lesson"/"My players are masochists" answer:
(Thanks to Zachiel for - unintentionally - reminding me to include this)
They arrive in the worst possible location. Covered in flames on the Plane of Fire, drowning on the Plane of Water, inside solid rock on the Plane of Earth, between two rotating cogs on Mechanus, five thousand feet above one of Arcadia's layers, etc. You'll probably never run into the problem of unspecified destinations ever again...
Maybe
The 9th-level Sor/Wiz spell teleportation circle [conj] (PH 293) says that
You create a circle on the floor or other horizontal surface that teleports, as greater teleport, any creature who stands on it to a designated spot.
But it's the DM's decision both how one goes about designating and what, exactly, is a spot. Here are some choices:
- Appearance: Designate a spot by describing a location. The greater, more unique, and specific the details, the more unlikely a false destination.
- Coordinates: Designate a spot by assigning it a latitude and longitude. Thus spots that move can't be designated.
- Crosshairs: Designate a spot by selecting a crosshairs; spots the caster's never seen can still be designated. Thus only locations large enough to have their own maps (e.g. a ship, a flying fortress) will have spots that can be designated.
- Name: Designate a spot by using its name, and employing the spell teleportation circle to travel to the named spot takes the creature to the location. (I suggest the location's most commonly used entrance.)
- Relative Location: Designate the spot by its relationship to something else (e.g. creatures, landmarks, objects, terrain features).
Also keep in mind that while the caster can't arrive off target using the 7th-level Sor/Wiz spell greater teleport (PH 293) (hence neither with the spell teleportation circle), he must still roll on the chart for the 5th-level spell teleport [conj] (PH 292-3) when the effect's used, and the possibility of a false destination or outright failure still exists if using the spell teleportation circle to teleport blind. (Despite the spell teleportation circle failing if its caster lacks familiarity with the destination, how one can become just familiar (rather than very familiar as described in the spell teleport) with a destination is never made clear.)
Best Answer
The spell says:
(emphasis mine).
Nothing says that the creature must appear in the same room as the destination circle, so RAW they would continue to appear in the nearest unoccupied space even if that was outside the destination room.
(Alternatively, a DM could rule that the teleportation simply fails in this case, though that would not quite be RAW).