We've stayed at a few. Here's the short take on the ones I can think of right now:
Reef Club: decent rooms, average AI food, good beach, lots of people, big resort, can be lots of walking to get to the dock/restaurants/bars depending on which room you are in, 15-20 minutes cab to town, upper stories have balconies to dry your stuff when you are through diving, bathtubs in rooms for a nicer gear rinse if you like, I've learned that i like to be closer to town so this is outside the area I would stay, if you don't want to leave the resort this is ok if you get a good price
Allegro: see Reef Club but a little nicer, too far from town for me now
El Presidente: see Allegro but nicer yet, too far from town for me now
Plaza las Glorias: my personal favorite for price and amenities, walking distance to town, nice pool, nice dock, nice bar, big rooms, fridge in room, balcony, bathtub, across the street from Chedraui (sp?) which is the Cozumel Walmart (easy to get a twelvepack and some water for the fridge), no real beach but they have a nice sandy area with stair access to the water, they were closed or are going to close for remodelling (not sure of dates), I like to stay here when price is competitive
Vista del Mar: boutique hotel down one of the alleys in town, balconies for outer rooms overlook the main road and the water (basically over the sidewalk), great for sitting on the balcony with a beer and people watching, balconies for inner rooms overlook the little shopping area in the alley, nice big rooms, shower only/no bathtub, fridge, continental breakfast included and delivered to room, I was worried that it might be noisy so close to the road but we didn't have any problems (traffic gets quiet by 10PM and we were up for diving in the morning before the cruise ship traffic started), inexpensive, I would stay here again on trips with just my wife and me, but not with a big group. Some dive shops won't pick up at town docks, check with them first.
Park Royal (the old Sol Caribe): private beach area, nice dock, below average AI food except for the breakfast omelete bar, nice pool area and bar, rooms can be nice but are somewhat rundown (eg shower might leak, or toilet might not flush until fixed, or cushions might not be on chairs for a day or two, etc), this place could be very nice but it's like they are scrimping on maintenance, bathtub, reasonably short cab to town, I'd have to check things out before I stay here again
Villa Blanca: upgraded rooms are nice, standard rooms are not, across the road from the water, no beach, we stayed in a standard room (mistake) which didn't have a balcony, upgraded rooms had balconies as I recall, bathtubs, short cab to town, I'd stay here again (in the upgraded rooms) if price was right
Fiesta American: nice resort hotel with everything you would expect, short cab to town, nice pool, no fridge, I'd stay here again if price was right
Casa del Mar: short cab to town, standard rooms are fine, cabanas are AWESOME, AI is optional and fairly good, decent pool and bar, I'd stay here again if price was right
Brisas, formerly Costa Club, formerly Hotel Fiesta Inn: HUGE pool and hottub, average AI food, short cab to town, nice rooms with balconies, bathtub, I'd stay here again if price was right
Summary: all have various things to offer. Reef Club, Allegro, and Presidente are too far out for my taste, but if you want an AI and don't care about leaving the resort, you can pick your level of "niceness" and price from these. Park Royal seems on the way down so I'd check closely before staying there again. The rest are within my "shopping" range.
There are lots of other places in Cozumel. Some of the review sites have great writeups you can use to compare.
I hope this was moderately useful!
Banon