General rule of thumb: do not buy businesses in Paleto Bay, the only exception is if you really like to run Doomsday Heist Act 2 finale, in which case this is the best location (terrible for all other acts). Yes, they are cheap but it's a pain in the ass to do anything from all the way north.
Locations in the city are always more expensive but the most expensive spots are not always the best spots!
I will try to not go into business specifics, for moneymaking guides see /gtaonline's pinned weekly Mega Guide thread.
Related: Beginners guide: Properties ranked by necessity

Apartments and garages

You can purchase apartments after reaching Rank 5. Location doesn't matter generally, though you might want to keep a few things in mind.
You can set apartments as a spawning location, you will spawn there when joining a freeroam session (not when leaving from a job).
There are apartments that can be used to set up heists, you may want to choose a location for your heist apartment near a highway access point as quite a lot of heist setups play in Blaine County.
Most apartments come with a garage, but you can also buy standalone garages, these are slightly cheaper than buying an apartment with the same size garage. You can not set standalone garages as your spawning location.

Offices

Buying an office will allow you to become a permanent CEO (as opposed to a VIP which is temporary). It also comes with a lot of purchasable extras. Interior layout is always the same.

• You can buy Accomodation which will grant access to a wardrobe and allow you to set this property as a spawning point.
• The gun locker extra is not that very useful, it allows you to set up a custom weapon loadout, hiding weapons you don't wish to use. This loadout only works in Freeroam and even there it will be disabled by some jobs (usually those that provide you with a specific weapon).
• The money safe is completely useless. Don't buy it if you are short on money.
• You can buy 3 separate garages with it, each hold 20 cars over 3 levels which are connected by stairs.
• There is also a Custom Auto Shop to purchase, it allows you to do Benny's customizations on your vehicles, though you can not sell your vehicles here (obviously).

Locations

The cheapest Office is Maze Bank West at $1m base price. It's a decent location but with a horrible roof helipad access (lots of stairs). Also most people will have this so if you play in populated lobbies, be wary of hostiles. Highway access nearby, a couple blocks away.
The next one is Arcadius Business Center in Downtown Los Santos, next to the Del Perro Highway at $2.25m base price. The roof access is slightly better than Maze Bank West but not by much. The garages can be accessed from the underground parking lot (where you can't sprint for some weird Rockstar reason).
Lombank West is 1 block away from Maze Bank West and it costs $3.1m. It has the best roof access of all of the offices. You can parachute straight to Del Perro Beach where you can spawn Personal Aircraft (stored in Hangar). It also probably has the best view of all offices. The garage access is terrible though, vehicles with a low base and a tendency to burn out (such as the Hermes) might get stuck trying to exit.
Maze Bank Tower in Downtown LS (near Arcadius) is the worst of the four in effectiveness. It costs $4m at its base price, it's the tallest office, meaning if you want to land on the helipad for quick entrance (press E on PC, probably honk interaction on controllers), you have to gain a lot of altitude. It also has the worst front door and garage access. The view is okay from inside. Roof helipad access has stairs, same as Arcadius.

(Special Cargo) Warehouses

Sourcing missions can be all over the city, sometimes even outside. Always try to get one with an easy highway access because even if you use a helicopter or other nefarious flying vehicle to get to the product, you may still have to drive it back to the warehouse.
Best locations for large warhouses are: Wholesale Furniture in Cypress Flats ($1.9m, cheapest), and Darnel Bros Warehouse in La Mesa ($3.5m, most expensive).

Vehicle Warehouses

9 locations. Can be spawning point by default. While the cheapest has a good highway access (La Mesa), it is a very popular spot for its price so you may have to be wary in populated lobbies, as players like to camp it to steal your sourced vehicles, or just to destroy them (watch for proximity mines). It's also in a gang neighbourhood so if shots are fired (by NPCs chasing you) you might get shot at by them, causing damage to your delivered vehicle. Some of the other locations are too far away from highways, anything on the southern side of the map is probably a bad idea.
La Puerta and Murrieta Heights locations are pretty good and no gang presence nearby. Davis is a very good location too but it's on the border of two opposing gangs.

Clubhouses

Will allow you to become an MC President and also run MC Businesses. You can monitor the production progress of your Businesses from here. You can also start MC Contracts (similar to VIP jobs, they even share cooldowns) and upgrade it with a Custom Bike Shop, allowing you to do Benny's customization on your bikes (where applicable). Naturally it also allows you to store 10 motorbikes. You can also set it as your spawning point.
Most MC Contracts take place in or near the city and even if your Businesses are in Blaine County (more on this later) you might want to have your Clubhouse in the city so you can more easily check on your businesses remotely (having an Arcade totally negates this need though, more on that later).
There are two interior layout variants, one with a second floor (such as Vespucci Beach) and one with only ground floor (such as Del Perro).

MC Businesses

For MC Businesses, the main thing about location is that you can sell to a local region (default price) or to a remote location (higher price, you want to choose this). If your business is in Blaine County, the remote location is in Los Santos city, and vice versa. For this reason having any businesses in the southern part of the map (Elysian Island, Terminal etc) or in Paleto Bay/Grapeseed is a very bad idea. Either buy them in the northern parts of Los Santos or in the southern parts of Blaine County.
So here is the list:

• Cocaine Lockup - Alamo Sea
• Methamphetamine Lab - Grand Senora Desert
• Counterfeit Cash Factory - Grand Senora Desert
• Weed Farm - San Chianski Mountain Range

OR

• Cocaine Lockup - Morningwood
• Methamphetamine Lab - El Burro Heights
• Counterfeit Cash Factory - Vespucci Canals
• Weed Farm - Downtown Vinewood

I omitted Document Forgery for a reason, it's not worth running it.

Bunker

Several upgrades, you can add accomodation to be able to set it as a spawning point. Similarly to MC Businesses you can sell to a local or remote location. Since all of the locations are in Blaine County, the remote sales will always be in or near the city. Therefore Bunker locations that are closer to the city are better, the best three are the following (sorted by price, Farmhouse is the best location-wise):

• Chumash ($1.65m)
• Route 86 ($1.95m)
• Farmhouse ($2.375m) ← this is the best bunker

Hangar

Hangars can be used to store your personal aircraft and to source crates which then you can sell. Two main locations are LSIA and Fort Zancudo, each have three hangar spots but you can only own 1 of the 6 in total. Upgrading with Living Quarters will allow you to set it as a spawning point.
Missions are all around the map but mostly somewhere in the northern parts of the city or the middle section of the entire map. Thus LSIA locations are really a bad choice if you ever want to do Hangar jobs. Otherwise it might be useful because you can only spawn personal aircraft, personal vehicles or CEO vehicles on LSIA grounds if you have a hangar here.
Having a Hangar in Ft Zancudo means you have a low level clearance, you will be allowed on the base and to fly over without getting shot down, this persists in any activity in freeroam.
Without question the best Zancudo hangar is "Fort Zancudo Hangar 3499". This is the westernmost of the three, it's the one with the middle range price with a $2.65m base price, the most expensive one in the middle of the military base is $3.25m and the cheapest on the eastern part is $2.085m.
The two main reasons why the westernmost hangar is the best:

• it's right next to the runway, meaning you can land easily,
• you can actually spawn your personal vehicles or CEO vehicles here. The other two Zancudo hangars have bad spawning points and the vehicles will spawn outside the base.

Facility

Facilities are used in Doomsday Heists. Majority of the preps, setups and finales are in or near the city and all Facilities are in Blaine County, similarly to Bunkers. Therefore it's a good idea to own a Facility somewhere close to the city. Upgrading with Sleeping Quarters will allow you to set it as a spawning point.
Good locations are the following ones (sorted by accesibility):

• Route 68 ($2.3m)
• Zancudo River ($2.1m)
• Lago Zancudo ($1.67m)
• RON Alternates Wind Farm ($1.855m)

The exception is if you are doing Act 2 finales a lot, in which case you may want to have Paleto Bay, but doing basically every other setup and finale will be a pain in the ass from there.

Nightclub

Again, highway access counts only for the very few setup missions (+getting the DJs the first time). If you have a good highway access, the location doesn't matter much, it's mostly area preference.
La Mesa, Strawberry, Del Perro are all great. Atmosphere-wise probably Del Perro, Strawberry and Vespucci are the best, with the two Vinewood locations if that's your thing.

Arcade

There are two arcades in Blaine County (Paleto Bay and Grapeseed), you should quickly forget about those if you want to host Casino Heists because the finale is in the city and it's a really long way, not to mention doing all the preps from that far. The only location I would advise against in the city is the Vinewood location (the most expensive) as it's really far from any type of highway, though Del Perro and Davis isn't really great either.
The best arcade is the cheapest in the city: La Mesa. It's very close to the Casino (great for finale) and to 3 highways, and since some of the preps take place very far in Blaine County, you will probably want to use the Avenger or personal aircraft (if you have any) to fly there. It's right next to the Los Santos Storm Drain, where you can spawn personal aircraft and the Avenger. The Terrorbyte spawns 2 blocks away as well.

Yachts

Yachts are probably the last type of property you want to blow money on, as it doesn't really provide much. I also suggest waiting for a sale on yachts as they are insanely overpriced.
 
There are 3 variants, the exterior differs slightly with every one of them and they come with different boats and helicopter. The GTA wiki has a very detailed list on them: https://gta.fandom.com/wiki/Galaxy_Super_Yacht#Models
The cheapest variant, the Orion is not worth it, in my opinion. It's only 1m cheaper ($6m) than the Pisces and it lacks a hot tub and doesn't spawn with a helicopter on the helipad (as far as I know?).
The middle priced variant, the Pisces ($7m) comes with a hot tub and a regular helicopter on one of the helipads (yes, this one has 2).
The most expensive one at a $8m base price, the Aquarius has a more expensive speedboat and helicopter spawning with it. It also has minor changes to the deck.
In my personal opinion the Pisces has the best layout, but I'm sure there are plenty of review videos on YouTube so you can decide for yourself.
 
It costs $25k to move the yacht every time, you can find a map with all locations (2-3 spots in every location) here. If the location where you yacht is already taken by another one when joining a session, your yacht will be moved temporarily to the nearest possible location. When you join a session where the spot your yacht was parked originally is free, your yacht will spawn in that location.
More on properties: https://gta.fandom.com/wiki/Properties_in_GTA_Online On gtabase.com: https://www.gtabase.com/grand-theft-auto-v/properties/gta-online/