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...
Though the Feywild might generally be depicted as a wondrous place full of life and vibrant colours while the Shadowfell a dark, dismal place of shadow and death, this hardly means they are (meant to be) inherently good and evil.
The TL;DR version is simply that evil certainly resides in the Feywild and good certainly resides in the Shadowfell.
The Feywild
The Feywild is home to many malevolent and typically evil beings. Hags, goblins, orges, giants, werewolves, blights... You name it. The 4e Heroes of the Feywild (HotF) suppliment even states:
These villains can be as fundamentally evil as devils or demon lords, and they wield powers of comparable might.
While there may not be a lot of information about the Feywild in 5e there is:
Seelie and Unseelie Fey.
[...] Seelie and unseelie do not directly correlate with good and evil, though many mortals make that equation. Many seelie fey are good, and many unseelie are evil...
There's plenty of evidence that can be found in the 4e books Manual of the Planes and HotF and the 5e DMG to suggest that the Feywild is certainly not full of only good creatures.
The Shadowfell
There seems to be less direct evidence that there's good in the Shadowfell but one quote in 4e's The Shadowfell - Gloomwrought and Beyond, I think, strongly suggests that even the Shadowfell is not entirely full of evil beings.
The Shadowfell is not inherently evil, but evil creatures are strong and plentiful there.
Evil may be abundant but it is never stated that only evil beings ever reside in the Shadowfell.
The Manual of the Planes also states:
For all the Shadowfell’s dismal reputation, it does have bright spots where those who fight against the malaise and the chill live almost ordinary lives. In fact, for many visitors to the Shadowfell, the plane has more in common with the natural world than it has differences.
Much like the natural world there is both good and evil.
Best Answer
From the description of the Feywild in the DMG (p. 49):
Because the sun never sets and is always in the sky, you wouldn't be able to see anything besides it. There isn't much information about the Feywild in 5th edition Dungeons & Dragons, so maybe someone who knows more about older editions can give you a more elaborate answer.