I have a somewhat different take from the others. First of all, I disagree that all canopy tours are the same. They're usually very similar however. They can vary greatly in terms of number of platforms, number of lines, height, length and speed of lines, how far into the woods you hike, how far from SJ you have to drive, how scenic they are, whether lunch is included, whether transportation is included, price etc. etc. Except for all those things, then yes, all canopy tours are the same. But Orange is essentially right that they ALL basically just come down to flying very fast through the forest canopy suspended from a cable.
My 2nd point is don't go expecting to see much wildlife while you're up in the trees. I haven't been to Tortuguero so that place might be a little different, but think about it. All that hooping and hollering that normally goes with zip-lines will scare most wildlife out of the area anyway (you might see a little while walking to the zip-line area if you don't have too noisy a group). OTOH, you can still get great views of the vegetaton and surrounding scenery, but even that is tempered by the fact that most platforms are surrounded by the vegetation and while you're on the cables that extend out into the open you'll be focused more on safety and that platform ahead of you than the surrounding scenery. Canopy Tours are better decribed as zip-line tours or adrenaline-rushes. If you want to really see canopy wildlife then go on a aerial tram tour or suspended bridges tour, which are more sedate, done more slowly and can be done with real naturalists guides rather than just essentially cable safety specialists.
Third point is most zip line tours are surprisingly short. A big part of the tour time is just getting out to where the offer the tour. I don't know about the zip-line tour on Poas that toad was talking about (though I'd like to hear more because I thought that troutfishing story was pretty cool), but most of these tours are MUCH further away from SJ. A full day tour from SJ typically only really has an hour or 2 of canopy time. That's why I generally prefer to go on them when I'm out touring the country than when I'm using SJ as my base. For example, if you're staying in Monteverde, Arenal etc. the zip line tours are right there and can be done in a couple of hours leaving more time to do other things during the day. There are also sometimes cost savings if you can drive to them or pass by them in your travels than when you pay for the ones that include transportation all the way from SJ. The Zip-line tours in the Jaco area are good examples of this. The Original Canopy Tour at Mahogany Park is only $45 for walk-ins but $75 from SJ (however that also includes lunch and a tour of the park). Chiclet's near Jaco charges $5 for pickup from Jaco and only $22 from SJ which might make you think that wouldn't be a bad way to get to Jaco until you consider they charge $60 (yikes) for the tour itself. The ones in Arenal, Monteverde cost only $40-45, which is high as you should ever pay unless you also get transportation.
Even if your tour is next door to where you're staying the actual cable time is shorter than even a couple of hours. Much depends on the number of platforms, lines and, not the least, the number of other people on the tour with you. Each cable run lasts at most 20 seconds and typically there aren't much more than 20 lines, if that. Most of your time will be spent walking out and up to the platforms, putting on your harness and waiting for others in the group to make their runs.
I may make it sound like I'm down on zip-line tours, but I'm not completely. I agree with toad that is a must-do for first-timers but something you might not want to do again. As it happens, I have done these tours again and again, multiple times and in multiple places. They can certainly be fun and something different to try. But for my money, after you've tried it once, I think there are much better things to do. The ATV tour is one possibility. I already mentioned tram and bridge tours for the true naturalists out there. But I'd put whitewater rafting right at the top. Actual river time can also be short (~3 hours) relative to how long you'll be gone but that is nearly all action packed. And it has a lot of repeat value. The 10th time you go is as much fun as the first.
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Some quick follow-up. I checked into toad's Poas canopy tour. The link is
http://www.colinasdelpoas.com/ingles/canopy.htm. The rates are $45 for just the canopy tour, $67 with pickup in SJ (that also includes lunch) and $80 if you also go for a morning visit to nearby Poas Volcano, which may be the best way to go despite the higher cost (ie really make a day of it). They pick-up at the Amon Plaza at 7AM and return around 2:30-3PM (time up in the platforms is still only 1.5-2hrs). They didn't mention if or how much they charge to use their rods for troutfishing. Maybe they throw that in or at worst I can't see them charging more than a couple of bucks for it.