Ken and I flew ourselves up to Vancouver for his birthday last week. It was our first international flight in at least ten years, with all the new US security stuff, and frankly it seemed so complicated I suggested we just land in Bellingham and drive across the border. But we figured out all the paperwork and it wasn't so hard after all. There's a variety of detailed guides for flying to Canada (I like AOPA's), here's the gist.
Weeks before the flight we got the plane documented for international flight. Proof of insurance, a radio operator permit for the pilot, a radio station license for the plane ($160), a customs decal ($30). Plus the usual plane documents for any flight. Nothing difficult but it requires a couple hours figuring out government web sites, then possibly weeks before the documents are shipped (ours came in a week). No one ever asked to see anything but the customs decal.
The Canadian border is pretty easy. When you arrive, they want a phone call 2 – 48 hours before the flight saying when you're coming. Then on the ground you call again from the customs box. In theory they may come inspect you and your documents, but for us they just gave us an arrival number over the phone. There's no specific border requirement when leaving.
The US border is more complicated. The big requirement is filing a passenger manifest with eAPIS for both your departure and your arrival. The web site is awkward (and broken in Chrome), so expect to spend some time. Fortunately you can file days in advance. The eAPIS filing gives you permission to leave the country via email; I also called the local customs office and they seemed confused that I was asking them. You do need to notify customs at your arrival airport 1 – 24 hours before you come back in, mostly so there's someone there to meet you. We arrived right on time and were done in 10 minutes at the plane: radioactivity check (!), passport check, customs decal check. Pretty easy.
Flights across the border need to be on a flight plan, both for the US and the Canadians. We went IFR so that was natural; if you go VFR you need a flight plan with a specific squawk code. Canada does charge for ATC services, apparently the bill is in the mail.