Since our planning was made SO much easier by reading lots of Trip Advisor ideas, I wanted to write in to help others planning their Costa Rica trips.
First of all, whatever you do, you probably can't go wrong. It is such a beautiful country I think anyone would be thrilled just to be there.
I've included information about our hotels, transfers, and a few of the highlights of activities in each place we stayed. Be warned, this is a little long....
1. Transfer from San Jose Airport to Arenal. Got a ride from one of Willy's colleagues (Rodolfo). Other than the rocky roads, it was a comfortable trip and we were greeted with a friendly smile ($130 for the trip). You can reach Willy at: firstname.lastname@example.org, and Rodolfo at: email@example.com. In our case, Willy booked us but then had a conflict so he hooked us up with Rodolfo. It worked out great.
2. Arenal - Stayed at the Erupciones Inn Bed and Breakfast ($70/night). Absolutely terrific. Not only is the view of the volcano great (though the lava flow was to the other direction, we still saw lots of puffs of ash), but the hosts really made the stay special. Jessenia and William were very friendly, helped us organize all of our activities, and even drove us to the Hot Springs one night, just because they could. The rooms were clean and comfortable (with A/C). I can't say enough good things. The place is a little far from town (about a 15-20 minute drive?), but taxis only cost about $8 each way, which wasn't too horrible.
-- The Raft Safari with Canoa Tours was our favorite activity. So quiet drifting along the river, seeing lots of wildlife.
-- Hot Springs. I would definitely recommend Tabacon over Baldi. On our first night, our volcano tour included a stop at Baldi, but we were pretty disappointed. They were playing very loud music, and we were very hungry and the food options weren't very good. If you like the "spring break" feeling, this is the place for you. If not, try Tabacon or even one of the other smaller Hot Springs places in the area. Tabacon was much classier, had a great swim-up bar where you could also order snacks and sandwiches (we got burgers that were truly some of the best we've ever had... but maybe that's because we were sitting in a hot springs while eating them!). It's more expensive but it's worth it.
3. To Monteverede... Jeep/Boat/Jeep transfer, hotel arranged it and it was fine, but nothing to write home about. In Monteverde, stayed at Arco Iris ($65/night), which was nice. It's so humid in Monteverde that we found it a bit hard to sleep (sheets felt moist all the time), but that was no fault of the hotel. I think it's the price to pay for visiting a beautiful Cloud Forest. If you really want to be comfortable, it might be worth staying somewhere with A/C instead, because that may cut down on the in-room humidity. Also, Arco Iris is located in town (which we liked because we could just walk to various restaurants for our meals instead of taking taxis), but it also looked appealing staying at one of the hotels closer to the Cloud Forest itself.
-- Do a morning guided tour of the Cloud Forest. The guides bring telescopes and really do look out for wildlife.
-- If you do a hanging bridge tour (we did Selvatura), I recommend hiring a guide. We did it without a guide and though it was beautiful walking up in the canopy, we were so clueless about looking for wildlife. Though you're never guaranteed to see any animals, I still think the chances are MUCH greater with a guide.
-- The Frog Pond is really a unique experience. I would go during the day for your tour to learn about the frogs, and then go again at night (you can go on the same or a different night on the same ticket), when the frogs are out... then you really get to see them in all their glory. If you can't go twice, I'd recommend just going at night (they are nocturnal animals).
-- Night Tour of Cloud Forest - there are a lot of different reserves to choose from, but I think doing one of these is a treat. Though we didn't see a ton of wildlife (and we were in a large group so it was hard to hear our guide), just being in the jungle when it was dark was an amazing experience.
4. Took Interbus to Montezuma. The trip was kind of long, but the ferry ride was beautiful (saw millions of pelicans). We stayed at Ylang-Ylang ($215/night which INCLUDES breakfast AND dinner for 2)... but there are cheaper and more expensive options), and absolutely loved it. I can't say enough nice things. This was our splurge, and we had planned to just relax here. It was perfect. It is a 5-10 minute walk down the beach, so it's a little isolated (they take you and your luggage in a jeep when you get there and when you leave). We stayed in an Oceanview Bungalow, which was the cutest thing. You constantly heard the loud ocean waves no matter where you were, and we loved that. Great to just sit on our little terrace and watch the waves. White-faced monkeys were everywhere. The pool was very pleasant... spent almost a whole day there and had our lunch brought to us poolside! The people were very hospitable and helpful. And the food was GREAT! We are still dreaming about that food, weeks later. For what you get, this place is a steal. If you don't stay there, it might be worth it just to have one dinner there.
We loved this place so much that we ended up canceling our one night in San Jose to stay an extra night at Ylang Ylang.
-- We mainly just relaxed (took walks on the beach, walked around town, went swimming), but we did go snorkeling at Tortuga Island. As far as snorkeling goes, the water wasn't very clear, but it was still a fun experience. Just be aware that if you book this through the hotel, you go an an excursion that includes 45 minutes of snorkeling, and the rest of the time you stay on Tortuga Island.... eat lunch and swim for several hours. If you don't want to be stranded on an island for hours, this isn't for you.
5. Our last day. Took a Sansa Air trip from Montezuma to the San Jose airport.... then off to the USA. Worked out fine (though make sure you have some cash available (colognes or dollars) because there is a luggage weight limit and an airport tax).
I know this is rather long, but I hope this is helpful for people. If you have ANY questions, feel free to ask.