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...
The Dominate Beast spell will end
There was a (somewhat confusing) developer tweet about this topic. Jeremy Crawford stated (emphasis mine):
In #DnD, the exceptional trumps the general. (No longer being a valid target trumps condition carryover.)
When a wildshaped Druid reverts to their normal form, we have those two conditions: the target changing type, and condition (charmed) carrying over. The target changing type makes it an invalid target which, as confirmed in the sage advice tweet, trumps the charmed condition carrying over.
Since the spell would no longer has a valid target once the druid changes back, the spell will end.
What about the other two Dominate X spells?
For completeness, let's run through the two other dominate spells.
Dominate Person requires a humanoid target. All official PC races are humanoid, so while the druid is in its normal form it can be targeted and charmed by a Dominate Person spell. If the druid wildshapes into a beast, its type changes to match that beast. So, the druid is no longer a humanoid, the target of Dominate Person is invalid, and the spell ends. In this way, it works in reverse of the Dominate Beast spell.
Dominate Monster works on any creature. Whether in beast form, humanoid form, or even in a Circle of the Moon druid's elemental form, the druid is still a creature. Thus, even going in and out of wild shape won't make the druid an invalid target. Since the target is still valid, the Dominate Monster spell will still have full effect, even if the druid wild shapes.
Best Answer
The entrance is the plant that's in range.
The spell states that a creature can step into the "target plant" and exit through the "destination plant". The "target" of a spell usually* refers to the creature, object, or location that's chosen at the time of casting, as described in the Spellcasting rules:
There are two important restrictions on targets elsewhere in this chapter: Range:
and a Clear Path to the Target:
The "destination tree" for this spell is chosen according to a different set of rules: it can be at any distance so long as it's on the same plane and you've seen it before. It isn't the target.
*Some sources, including on occasion the published rules, irresponsibly use "target" to refer to anyone or anything that's affected by a spell, such as creatures within an area of effect. This usage is confusing and I would recommend against it.