Note: written Feb 14th 2011. There is a HUGE complex the Ecuadorians have built that is not open yet, but someday will be and currently it's rather difficult to find the Ecuadorian Aduana and Migrations offices. If you're heading north and it's open ignore the rest. If you're heading south and the Aduana listed below isn't staffed any more then ignore this. The border is open 24 hours. We went around 10 AM on a Monday and there was essentially no-one using it (either time).

This is for the border crossing at Huaquillas, Ecuador and Zaramuilla Peru

The Aduana is about 6 k before the border at
S 03 31.947
W 080 10.696
Heading south look for the twisted black and white remains of one of those gates they can raise or lower to block traffic. Directly to the left of that is the Aduana. The entrance is just south of that on the left. If you see the Paradise Hotel (which you've been seeing small billboards for over 20k) you've gone too far.

Coming north hang a right at the roundabout, go approximately 5km and look for the Paradise Hotel on your left. The Aduana is just past it on the right.

Migration Office:
Heading south hang a right at the roundabout, go through the toll booth (motos can just skirt to the right of it) and turn around at the first break in the divided road. It'll be on your right just after you turn around.

Heading north hang a left at the roundabout and follow the same instructions.

NOTE: do NOT ask the people at Migrations where the Aduana is. They all (asked 3 different people) will direct you to the huge complex which is not open and none of them will believe you when you tell them it's closed.

__________________
-Dachary & Kay
http://www.CorporateRunaways.com

We crossed from Peru to Ecuador today, Dec 7, 2011, so here's the situation as of today.

First off, the bypass road completely misses the towns of Zaramilla and Huaquilla, so pay no attention to guidebooks claiming this as "the worst border crossing in South America." Perhaps for backpackers searching for buses, it's bad, but for moto-travelers, it's easy.

Checking out of Peru is straightforward. Migracion and Aduana are next to each other.

The big Ecuadorian border complex is partially open. At the end of the first building, there is a SOAT office where we bought a month of insurance for $3 for each bike.

Then, two buildings further on is the immigration office.

Aduana (customs) is still in the old spot at the waypoint listed above (thanks, Dachary & Kay ). After leaving immigration, continue on and head towards Machala/Guayaquil at the roundabout. Traffic is diverted off the road for a customs check at the office, so you can't miss it. And there's a little shop across the street where you can make necessary copies.

No problems and little traffic at the border.

-Laura
Ridingaround.wordpress.com

Update from the 31st of july, 2013. Crossed from Peru into Ecuador:

So the first big complex you'll encounter at the border (Peruvian side); ignore it as it's only for people entering Peru and drive on! You'll see another one, kind of the same, where you have to go to the Peruvian Immigrations and Customs, and then to the Ecuadorian Immigrations (all in the same complex). Afterwards, the Ecuadorian Customs are indeed where Laura says they are; some 3-5km further up on the Panamericana!

Try to be there before the big busses around midday, as immigrations is incredibly slow.