Last year Ecuador closed its borders for a few days while the President was being kidnapped and all that. Sounded pretty hectic. But by the time I got there (two weeks later) everything seemed fine and easy.
You haven't said which way you're going (Peru->Ecuador or Ecuador->Peru) so I'll assume the former, since it's what I did, and you can reverse if necessary ;)
I was short on time, so had bussed from Lima to Máncora, just in time for the full moon party at The Point Hostel. Quite the experience, I assure you. Anyway, from there you have two options - do it yourself, or do it with a 'guide'. I was grouped up with two others at the time and by 'guide' it's just a guy who shows you where to walk at certain points, but he did make things a lot easier, I'll give him that.
There is a bus from Máncora TO Quito, and certainly towns before it, but as I said, I was short on time. So the bus goes up north along the coast to Tumbes. There it paused briefly, before heading to the border in Zarumilla. Here's when it gets fun.
The Peru part was easy enough. Go in, get exit stamps, avoid the usual money touts swarming around. Then we headed over the river border to the town of Huaquillas. We had to be ushered around and pointed at a window, get stamped etc, and then take our bags out the bus. No explanation of what was happening, but then the bus drives off. A little concerned, we look to our guide, who is already waving down a taxi for all of us, but nearly forgets one as we're about to drive off.
It weaves around the streets, and this is where the guide earns his keep. With no Spanish, you'd have a lot of difficulty finding what turned out to be the domestic bus terminal. He dropped us off, gave us a bag of food for the ride (woo!), and vanished.
We had to look at the schedule and our tickets to realise we had an hour. The guys at the terminal stored our bags for us for free while we wandered the streets (evening time) through some markets, bought some more food, joined up with some Germans and another Kiwi who were coming as well, and then finally boarded the next bus to Quito. A few hours later (well, like 10), we were there!
Conclusion: the border town is 'sketchy', but only in behaviour and confusion - we felt just fine wandering around in partial darkness, in a group at least. But had zero problems in the end, which fits with my travel philosophy of assuming the best ;)
In terms of the other crossings, I can't offer much more, but almost every single traveller I spoke to coming south or heading north had or was going to use this route. So you'll almost certainly see other travellers to group up with if you wanted.