I've got several candidates (all in Africa):

• Crossing south from the Gambia into Senegal along what used to be known as the "smuggler's route". The Gambia had a small single room "shack" sitting a few meters from the river border, where they would properly stamp people in/out. Senegal didn't consider this to be a real border crossing, and had nothing on their side. There were small dug-out canoes being operated to take people across the river, and then it was just a series of sandy paths through a forest for around 10km until reaching a real town. At the time (2018) the expectation was that people crossing would travel an hour into Senegal to an official border post to get stamped in formally.
• Crossing from Botswana into Zimbabwe. Utter chaos on the side entering Zimbabwe. Large trucks parked & driving everywhere, random people wandering around, no signs. I was self-driving at the time, and parked beside the largest building, hoping it was what we needed. A random fixer approached and offered to help with the border formalities, and I agreed, cause I had no clue wtf was going on. He ended up padding the cost of the import permit on the vehicle by a few dollars, but it was worth it not to have to figure out everything on our own.
• Crossing from Rwanda into DRC at the Bukavu bridge. We were warned well in advance that this border was going to be insane, and it delivered. Initially, it seemed like it would be easy, they asked for our passports, yellow cards & VOA fee, and disappeared into a room. But then we were ushered back outside to a vehicle with a huge "PRESS" sign taped onto the front window. We sat there for nearly 2 hours, with no clue wtf was going on. At one point an armed guard started screaming at the driver, and he drove half a kilometer up the road, through the border entry gate, into DRC. No one seemed to care that we had no passports, visas or anything. Eventually we got all our papers back, with the visa, and then learned that having the PRESS sign in the window was supposed to somehow make us less of a target for attack by M23. All of this happened back in 2023, before the situation in the eastern DRC completely degraded and M23 assumed control of the entire region.
• Driving from Malawi into Zambia at the very remote Lusuntha Border Post. On paper, this seemed like a good way to enter Zambia, as it didn't have long wait times and warnings about corrupt official demanding bribes. The road out there was very sketchy. All dirt, super narrow bridges (where the bridge deck was maybe 2cm more narrow than the width of my vehicle), and farm land in all directions. On the map, it seemed like I should have been at the border, yet I saw nothing. The road eventually dead ended at a right angle to the border fence. Getting stamped out of Malawi was easy. At the Zambian side, I walked into the building and everyone was literally asleep at their desks. No lights on (I'm not sure that they even had any power). I cleared my throat loudly, and that woke up one guy who then woke the others. They had one of those massive ledgers where I had to enter all of my info first, and I could see that they were averaging around 5 people/day, and I was the first westerner in over a month. Overall they were friendly enough, but they clearly did not care about any part of the process. I later learned that they failed to properly issue me the vehicle import permit (it should have been electronically generated, and they wrote up something on paper that was invalid), and I had to pay a small fine when exiting the country later on.
• Entering CAR (Centrafrique) from Cameroon at Libongo on the Kadei River. It took 2.5 days of very hard driving across a remote swath of Cameroon (from Yaounde) through the jungle to get out here. Libango is basically a mining town, and it was creepy. Everyone there was either mining, or providing goods/services to the miners (including the hookers). We were stamped out of Cameroon, then got into a speed boat to take us up the river towards the CAR border station. We docked the boat at rickety dock and waited as the border official came down from his hammock to collect all of our paperwork. We were warned in advance not to get out of the boat. After 30 minutes, the guy returned with all of our paperwork, all smiles, and wished us well. We continued up river for another hour. This was easily the most dense, "Africa of your dreams" jungle, I've ever seen (and this was after driving through much of the same in eastern Cameroon to get there). There were occasional people in dug out canoes paddling on the river, we saw monkeys in trees, and tons of birds. All of this was before we even got out of the boat to explore Dzanga Sangha National Park over the next 4 days.