This is the first and unfortunately, due to my broken leg, the last of my hotel/hostel reports I'll be making from my trip through Central America. This isn't a list of every place we stayed every night, just the ones at 'destination' places we visited. I doubt anyone is interested in the anonymous hotels we stayed at in between these spots (and if you are, I don't really remember their names or locations, so you're out of luck anyway
Zacatecas: Here we stayed at the Hostal Villa Colonial and I can't recommend this place highly enough. They've got rooms for every budget, from dorms to very nice doubles with TV and private baths (don't worry, you won't need AC here, it gets COLD at night). It also has free wi-fi internet, two kitchens you can use, free water coffee and tea, a very good book exchange, and a beautiful rooftop terrace with a great view of the city. The owner, Ernesto, is very friendly and accomadating (the day we arrived they were fully booked, but he got us set up with a place around the corner until he had room in the hostel) and he speaks very good English. Unfortunately, this place has no parking. We parked on the street right in front of the hostel and, over 10 days, my father had the cover stolen off his bike (but nothing else, despite the fact that the keys were sitting in the ignition when the cover got nicked), but nothing else happened.
If you want a hotel with parking for motorcycles, I'd highly recommend the Hotel Plaza del Carmen. I didn't stay there, but I did meet the owner, Manuel. He owns a KLR650 and was very helpful when I needed to replace the shock on mine. He parks his bike in the lobby of his hotel, and you'd be welcome to park yours there as well.
Guanajuato: We stayed at the Casa Bertha and, again, I liked this place very much. Guanajuato is an expensive town and, for the money, Casa Bertha is a great deal. They also have a range of rooms from nice doubles to dorms, a kitchen with free water and a nice terrace. Parking-wise, they do not provide parking but the hotel is located off of a pedestrian-only plaza where we were informed it was fine to park our bikes (there were certainly plenty of local motorcycles parked there). We left them there for three days without incident. If you want more formal parking, there are several parking garages in Guanajuato, both above and under ground but they are very expensive, from what others told me.
Oaxaca: The first place we stayed here was the Paulina Youth Hostel. They advertise themselves as the cleanest hostel in Oaxaca and they're right. It's so clean there I'd label it sterile. Very organized, very clean and very soulless. They had doubles but we stayed in the dorms because the woman at the desk said the doubles were loud (being right on the street). The dorms were very quite. The Paulina has an agreement with a parking garage two blocks away where you can park for no extra charge. After a few nights there my father and I moved into a homestay, and it was a much better deal. We stayed in our own room in a nice house with breakfast and lunch included for less than we paid at the Paulina. And, since it was an actual house, secure parking was no problem at all.
Palenque: We stayed at a hotel/restaurant compound just outside the gates of the park called El Panchan. There are about half a dozen hotels of various sorts and a few restaurants inside the compound. We stayed at Maragrita and Ed's which was very nice and very reasonably priced (double w/o AC for 200 pesos). El Panchan has a bit of a party reputation, but when we were there it was very laid back. Party or not, Margarita and Ed's is set back so far in the jungle I doubt it would be too disturbing there. We parked the bikes outside next to the hotel and felt perfectly safe leaving them there. The compound is gated and there aren't a lot of people coming and going (at least at the end of October). The main restaurant at El Panchan, Don Muncho's, also deserves mention because it is really freakin' good and very reasonably priced.
Panajachel: Here we stayed at Mario's Rooms. We'd heard good things about this place, but I didn't find it to be all that special. It was fine, but nothing especially worth noting. They let us park our bikes in their foyer, but it was not too easy getting them in and out, and the foyer had no doors so I'd only label it semi-secure.
Antigua: We stayed at The Yellow House, which our guidebook said had parking. It does not, but there is a private lot at the end of the street that was not too expensive (70 quetzales/day, but since we were leaving them there for 12 days we paid the monthly rate of 300 quetzales, which was more reasonable. Everything seemed up to negotiation, and I'm not a great bargainer, so you might get a better deal). The Yellow House itself was a very nice place to stay. Cheap dorms, doubles with TV and neat 'cabins' up on the roof. Very nice, English-speaking staff, clean, free internet and water and a good breakfast included in the price. It's also pretty laid back (but still socialable) , not a giant backpacker party. One thing to note, if big friendly dogs or hyperactive 7-year old kids bother you be aware that the Yellow House has one of each. Also, there are no rooms with private bath and there can be lines for the shower in the morning.
Granada: We stayed at the Bearded Monkey Hostel. Definitely a backpacker hangout, and I mean this in a very good way. The place is, by far, the largest hostel I've seen in Mexico or Central America. Four big dorm rooms opening out onto a large courtyard and several double rooms are tucked away in back. They have free internet (broken when we were there) a nice TV room and lots of places to hang out. It has a lot of people up talking, but it wasn't a loud party. The food there is also very good. They didn't have parking, but you can park inside the firestation across the street for a very reasonable price. Be aware, though, the firemen said it'd be 30 Cordobas/night but, after we'd parked the bikes, unloaded them, covered them and locked them they upped the price to 50/night. We argued for a couple of minutes and the price went back down to 30/night.
Ometepe: Here we treated ourselves to staying at the Villa Paraisio. Reputedly the nices place on the island we had no intention of staying there until a giant thunderstorm opened up on us while we were trundling down the dirt (now mud) road to the southern part of the island. The Villa Paradisio was the first place we found and, luckily for us, they had a room. Also, luckily for us, a regular double room is not a bad deal at all. All that and the food is amazingly good. We're parked in their front parking lot, but considering this is a tiny island with only four ferries a day to the mainland I wouldn't worry about the bikes no matter where they were parked.
I do need to make one more note about the Villa Parasio. Ometepe is where I dumped my bike and broke my leg and the people at the Villa Parasio went far above and beyond the call of duty in helping me out. When the island's ambulance was unavailable it was their truck that made the two-hour drive to where I crashed to pick me up. It was their driver in San Jorge that got me to the hospital and it was their guide on the mainland-Hector-who was unbelievably helpful in translating and fascilitating all the stuff that needed to be done to get me what I needed. They also managed to extricate our bikes from the far end of the island where we left them and kept them in their lot until my Dad could get back and move them to the mainland. Without their help, I would've been in a lot bigger pile of crap than I was on Ometepe.
Hope this is of some help to y'all.