So it sounds like you want to add some thought, memorability and danger into the travel time, but you don't want them to meta-game things so that they are overpowered by the time they reach their destination. You don't want them 'hanging around' these locales longer than necessary, over-foresting the fiendish-squirrels to extinction for XP. I would handle this a couple of ways:
Low treasure for random encounters
If you award XP by the book, with no extra 'story point awards' and keep treasure low to Nil (sorry the Dire Lions did not drop 100gp and a pair of bracers +4), I don't think they'll stay there long or advance too quickly.
Keep the CR level of the encounters in the Yellow Zone
I would keep it maybe at or a tick or two 2 above the party level; whether from sheer numbers of opponents (a large # of giant ant warriors) or quality (1 hill giant) or circumstance (see weather below). I think that most wilderness encounters are things that players should at least think about avoiding or fleeing from. These are encounters that should bloody them if they take them head on.
Roll encounters 'randomly' in advance
Roll a few (2 or 3) wilderness encounters in advance and write the results down on notecards so you at least have some idea of what they are going to be ahead of time. Helps to think about 'if this goes down, here's how it will go down'. Then for the encounter check, you are rolling to see if the encounter occurs (not IF it occurs and WHAT it is; you already know what the WHAT will be. You can also determine the encounter distance in advance or things like that)
Roll the Weather in advance
If there is going to be a lot of overland travel time expected, actually roll the weather up for the next three months. This (can) add a lot of flavor to encounters that do happen. Fighting a Troll in the middle of rainy deluge (or even a dry spell where the whole forest is ready to go up like a matchbox) can be a whole different ballgame from what players are used to. A swarm of Gibberlings in dense fog banks could also be unnerving; it is the Wilderness, so play up the different conditions that can happen there.
Track player supplies, and make foraging a dangerous challenge
In many of the classic fantasy novels, starving or dying of thirst is a real problem. This gets overlooked too often I think, or just 'handled' by someone making a Survival check at +10 or the like. Set some higher DC levels for different areas for foraging. When foraging, check for random encounters. (you might not be the only predator tracking that wild boar...) If an area has a low forage yield, it may be inhospitable, or there may be a real 'top of the line' predator around causing the imbalance.
Use Stalking encounters
Quite a few monsters (natural and unnatural) tend to stalk their prey for quite some time and 'wear them down' preventing them from resting, picking off stragglers. Wolf packs, Meenlocks and many others might come to mind here. Being in the wilderness means there is no safety. You may know 'something' is out there, you might even skirmish it into a quick retreat, but that doesn't mean it isn't going to come back a little later. Stalking is probably waaay underutilized in the wilderness.
Make it a challenge for the characters to exist in the Wild, and they'll not only remember it, they may feel relieved to get to where they are going.
As you have said you are willing to consider Spelljammer rules, I can pull a few quotes in for you that might help clear this up.
From Spelljammer Core Rules: Book 2, Concordance of Arcane Space, p. 17
Clerics in Space: A cleric may not regain spells above 2nd level while in the phlogiston. This is because he remains out of direct
contact with his deity.
A cleric who enters a foreign crystal shell is similarly restricted.
The only exceptions to this occur when a cleric's deity (or a similar
power) is recognized in the foreign shell or the cleric casts a
successful gate spell, affording his deity access to the foreign
shell.
Any god or power is considered "recognized" within a sphere if he has
worshipers and/or an organized church anywhere within that system.
This does not mean that a PC cleric can move into a shell and
automatically establish a base of worship for his god. For a deity to
be a recognized power in any shell, he has to have an established
base of worshipers somewhere in the system.
Additionally, the same rulebook adds the following spells on page 22
Contact Home Power (2nd level Conjuration)
The user of this spell establishes a tenuous link through the Astral
Plane between his present location and that of the power he venerates.
This link permits the priest to regain his spells as if the god is
recognized and venerated within the sphere.
The duration of the spell is one week, as long as the cleric remains
in the same crystal sphere in which he cast the spell. Passage into
another plane (even the ethereal) will break the spell.
and
Detect Powers (2nd level Divination)
[This spell] allows a cleric to determine if there are friendly gods
and/or other powers within a crystal sphere so that he may recharge
his higher-level spells within its borders. It also reveals if the
god(s) revered by the cleric are worshiped within that sphere.
In this case 'friendly' is defined as 'same basic attributes and portfolio' or possibly 'same god by a different name.' As two examples...
-Paladine and Bahamut are the same god, but known by different names and roles in two different spheres.
-Reorx and Moradin are two distinct gods (from Krynn and FR respectively), but they are sufficiently similar that a cleric of one could receive spells from the other.
So, if you take these pieces of information into account, it gives you the following answer:
When you are on a different world within the Prime Material Plane, you may only regain spells up to 2nd Level unless
1: Your god has an established base of worshipers on that world, or on another world within the same Sphere. This implies that the other gods in the system don't actually get a direct say in the matter...though they could certainly stamp out 'heretical religions' if necessary.
2: You use Detect Powers to locate a friendly deity (or your own) and refresh your spells via them.
3: You use Contact Home Power on a weekly basis to 'phone home' and keep that connection open so you may reload your spells.
4: You use Gate to connect directly to your deity's domain and refresh your spells from them directly.
Now, I do not have access to the Planescape books, so I am not 100% certain that this isn't contradicted somewhere in those books...but if you are willing to abide by Spelljammer rules, that's how it works.
Best Answer
118 to 212 days, give or take some encounters
Travel times depend reliably only on one thing: the existence of a phlogiston river. Helm operator level matters for ship speed only at tactical speeds, not over long distances, so we can disregard navigator level (Spelljammer boxed set, Concordance of Arcane Space, p. 35). Rivers have directional flow, so only rivers that flow from your origin to your destination are useful; few rivers are bidirectional. Travel through the disordered, non-river phlogiston is dangerous and more than twice as slow on average, assuming you arrive at all.
Greyspace and Realmspace are fortunate: a river flows bidirectionally between them (sidebar spanning pages 86 & 88), making travel possible and relatively easy from Oerth to Toril. The time to travel through the phlogiston from any Sphere’s wall to any other Sphere’s wall is variable, depending on unknown factors, and ranges from 10 to 100 days (p. 54) (disregarding, as you say, whether conveniently-placed portals are currently available).
Travel within the Spheres depends on whether you encounter trouble that delays you (p. 72–3), and where you enter the destination Sphere (which is random), which determines how far you are from the destination planet. We'll ignore encounters for now in order to determine a baseline of travel times. Where you leave your origin Sphere is presumably the closest sphere wall to the origin planet's current location, unless factors interfere with the direct route, so we can use minimum distance there.
Spheres have a diametre twice the orbital diametre of the outermost planet (p. 52). Per Appendix 2: Travel Times, Oerth to The Spectre is 40 days, and Oerth is the centre of Greyspace, making it 80 days to the sphere wall. In Realmspace, Toril is the third planet out, and its minimum travel time to H’Catha is between 14 days (closest approach) and 18 days, giving a minimum days’ distance from a random location on the sphere wall of 28 days, or (given that Toril is 2 days from the Sphere's primary/centre, an orbital diametre of 4 days) 28 + 4 = 32 days at worst if you enter the Sphere on the far side of Toril’s orbit. For such a long distance we're ignoring takeoff and landing times in gravity wells, since they're on the order of tens of minutes (p. 53) and are less than a rounding error.
Given convenient portals in both Spheres’ crystal walls, and given a lack of interesting encounters (both big ifs), we can calculate a baseline travel time from Oerth to Toril at 80 days (Oerth to Greyspace wall) + 10–100 days (phlogiston river) + 28–32 days (random Realmspace entry point to Toril) = from 118 to 212 days.