New Town:
Grinn House: Calama y 6 de Deciembre (New Town). Located in the New Town at the end of the bar & restaurant-filled Calama St, this hostel is brightly lit, immaculately clean and features some of the most comfortable beds and blankets you'll find in any hostel in South America. Dorm rooms for 4+ people (if there isn't much traffic you might even get a room to yourself). The double suite has it's own private bathroom and cabinets for your belongings. Open kitchen and fridge for guests. Plenty of hot water, free wi-fi internet, and optional laundry service and breakfasts. Very friendly owner and staff are happy to help with directions, activities, tours, cabs, etc. $7 per person with shared bath, $20 double private suite.
Hostal Marsella: Ríos N-12-139 (2035) y Espinoza (Alameda). Located between New and Old Quito, just up the hill from Parque Alameda. Plenty of clean rooms with sitting areas both inside and under a new glassed-in ceiling on the rooftop (with views of the Basilica and the Panacillo/Angel.) Hot water, free wi-fi internet in the common areas, laundry service, large breakfasts ($2-$3). Door is locked 24/7 for security and the very friendly owners and staff are happy to help with directions, calling cabs, etc. Great spot away from (but within walking distance of) the much more touristy Mariscal Sucre. $7 per person with shared bath, $10 private.
Old Town:
The Secret Garden: Calle Antepara E4-60 y Los Rios, San Blas, (593)2956 704 or (593)3160 949,. Offers a roof terrace with a great view and herbs grown by the volunteer staff. Moreover there is a jaw dropping and wonderful view of the older section of Quito. Has a great in-house travel agency Carpedm Adventures to help sort out Galapagos, Amazon & more. There are fires nightly and the staff cooks three course meals every night, the hostel also offers breakfast for $2,80.
Hotel Huasi Continental: (Close to the crossing of Flores and Sucre.), Calle Flores 308. Nice and clean hotel in the old town with helpful staff. Note that some of the rooms facing the street can be a bit noisy. Singles from $10.