Island hopping in Honda Bay alone, for instance, will eat up half of your day so try to get up early and be at the wharf before 9am to beat hundreds of tourists that crank in. You know what they say about early birds getting the worm. Boat rental starts at 1,300 and they only have a handful, so when these boats are occupied, rental fees get a little higher. Don't asky why, I myself don't know the reason behind it.

How far is the Honda Bay Wharf from downtown Puerto Princesa?

It's a relatively short drive from the city, about an hour or less. You can rent a trike (300-500) but hiring a van is also a good option if you're in a large group (1,200 per pax). The van will wait up for you until you're back from the tour and will take you back to your hotel. One advantage about hiring a van is it usually comes with food (with additional fee of course - 200 per person) - owner's recommendation. Food will be prepared by a caterer and will be picked up on your way to the wharf. Best bang for your 200 pesos once you see the spread of sumptuous food which includes prawns, crabs, veggies and grilled pork. Alternatively, if you chose a DIY tour, you can buy food from a nearby restaurant.

Our food

How long exactly does the island hopping tour take?

Depends on how long you want to spend on each island really. There are five stops in the tour, minus Snake Island. We're told that a businessman bought the island and closed it to public so it's off-limit for God-knows-when. Your rented boat will take you to Pandan Island, Starfish Island, Pambato Reef and Luli Island, in no particular order and according to your preference.
Pambato Reef is not an island though, but a reef, discovered by a local fisherman some years ago. There's a floating walk-way and large raft at the area, which can accommodate a specific number of people. The reef is a good introduction to the diverse marine life of Palawan although there aren't much fish around the vicinity.

Is there an entrance fee to each island?

Yes. It's 50 pesos per island, exclusive of snorkeling gears. You can rent one at the wharf though (100). Van drivers will lure you to rent them at a rental shop along the way, you can politely refuse the offer (150) because these gears can be rented at a much cheaper price at the wharf. Be mindful of your snorkeling gear, if lost, you'll be required to pay a few thousands.
Say, I don't want to island hop and just stay on one island, which island would that be?

Ah, choosing the best island is a tough decision because each one has its own distinct characteristics that can appeal to one's taste. So it comes down to your personal preference. For its rich underwater life, I enjoyed Pandan Island the most. It's ideal for beach combing and snorkeling  There's a specific spot in the beach where various fishes will come near you  as long as you have bread crumbs to offer them. I've never seen fish in such multitude. They're a sight to behold.
Luli (short for 'Lulubog-lilitaw') Island comes in second for my top choice. What I liked about this island was the sense of abandonment and isolation it harbored - from the old beach houses to the worn-out shelter floating above the clear water at the other side of the island. It's probably due to this reason that some island hoppers skip Luli and the fact that there's no coral reef here. 
What it had which other island didn't was the diving platform perched on the edge of an elevated kiosk. It's about 12 feet high, pretty safe for diving off. A stretch of narrow, White-powdery sandbar that extends to both sides was an addition to its charm.
Starfish Island is called as such because of the abundance of starfish in the island. During our stay here however I only saw one, courtesy of our jolly and helpful guide who plucked it from the shore shortly after having our lunch. Snorkeling is best done here when high tide otherwise you'll find it hard to wade through waist-deep water with sharp rocks at the bottom.
Looks like you enjoyed Pambato Reef the least.

No, that's definitely not the case. But in hindsight, maybe I didn't enjoy it as much as I did with the three stop-overs. You can only snorkel at Pambato Reef and again, marine life wasn't that impressive compared to snorkeling sites in Pandan or Starfish. Still, it's a good pit-stop.

Can you spend an overnight on these islands?

Not that I know of although each island can be a good spot for camping, except perhaps for Luli since it gets submerged during high tide.
Did it take you a whole day to complete the tour?

Not really. We were back at the wharf at around 3 after braving strong lashing of rain in the middle of the bay. I told my friends we should get going when I saw dark clouds looming over the horizon but they were too engrossed with snorkeling at Pandan Island (couldn't blame them!). I was scared for my camera than for my own safety. Good thing the current wasn't that strong so we made it to the wharf safe and sound.
 How much did you spend in total?

It's much cheaper I guess when you come in group as opposed to going alone. Here's the breakdown of our expenses.

Van = 1,300 per pax (216 each) 

Boat rental = 1, 300 (216 each)

Food = 1,200 per pax (200 each)

Entrance fee = 1,200 (200 per person) 

Snorkeling gear = 900 (150 per person)

Miscallaneous:

 500 (83 each) tip we gave to our boat man

 200 (42 each) fresh crabs we bought at Luli Island

Total =  6,600 (1,100 per person)

     

Not bad huh.

Yeah, and I believe that's way cheaper compared to purchasing a package tour.

Any other tips?

Don't forget your hat, shades and sunblock lotion as it can get pretty hot out there especially during mid-day when the sun's scorching. Apply generous amount of sunblock and bring towel or malong so you can lie down on the beach without burning your skin. Bring dry bag or waterproof case to protect your gadgets like cellphones or camera.

And lastly and most importantly, have fun!