We didn't booked anything in advance. We just arrived and found a place. There are plenty. 

We payed 250 Dirham (around 50 Euros) for a night (including breakfast). 

Recommended number of days: 1-3 days

We slept at the Ibis Hotel and payed 60 Euros per a night for a couple. 

Recommended stay - 1 day, at most! (depending on you flight)

Best Western Odyssee Park

Boulevard Mohamed V, 80000 Agadir

http://www.booking.com/hotel/ma/odyssee-park.en.html?sid=a446ff4cb08a507cc82d7b25e56acc57;dcid=1;checkin=2013-05-23;checkout=2013-05-24;srfid=1e5fa1ee3ca8e1e5892d9cf6b45363d50dec53d3X4

Excellent hotel, great location, western style breakfast.

We paid 50 Euros per night including breakfast. 

Recommended number of days: 1-2 days.

We planned staying in Rabat for our first night of the trip. From searching on the web, I saw that there are variety of lodging options. Some are quite cheap and some aren't. One of the ways to stay in Morocco is in a Riad - a kind of boutique hotel or high level guesthouse which has up to ten rooms. I booked our first night through www.booking.com based on user reviews. 

This site was quite essential to us during the trip - before reaching our next destination, we chose our next accommodation with it.  I chose places with user ratings of 8.5 and above with an average cost of 50-70 Euros for a couple, including breakfast. Take into account that there are additional tax of a few Euros for night per person.

I'll give specific recommendations about Riads under each city. 

Rad Alya

8 Bis Derb Guebbas.Quartier Batha. Medina -Fes Maroc, 30000

http://www.booking.com/hotel/ma/ryad-alya.en.html?aid=304142;label=review_am;sid=a446ff4cb08a507cc82d7b25e56acc57;dcid=1

Undoubtedly the best Riad we've ever been to - in terms of rooms decoration, service and people.  The help, service and care of the staff was beyond expected and contributed a lot to our Fes experience. 

We paid 65 Euros. 

Recommended number of days: 1-2.

Riad Lila

21,Derb Dabachi,Derb Mouly Abdelkader, Medina, 40000 Marrakech

http://www.booking.com/hotel/ma/riad-lila.en.html?aid=304142;label=review_am;sid=a446ff4cb08a507cc82d7b25e56acc57;dcid=1

We payed 60 Euros for a night including breakfast.

Recommended number of day: 3-4.

We slept at:

Riad Dar Alia, 15, Rue El Hout - Bd Des Consults, 20000

http://www.booking.com/hotel/ma/dar-alia.en.html?aid=304142;label=review_am;sid=a446ff4cb08a507cc82d7b25e56acc57;dcid=1

The Riad is located withing the old city in an alley. From my experience, it wasn't easy finding those riads, but usually one of the locals led us easily to them in exchange for several Dirhams. 

We payed 55 Euro for a night including breakfast. Number of recommended night: 1-2 days.