Sosnovka Vacation Hotel 2800.00 RUB
Hotel and recreation center in the suburb - near the shore of the Ob' sea. In 15 minutes by road from Akademgorodok and in 40-120 minutes from city center (depends on traffic). There are rooms for 800 RUB w/o shower. Sosnovka also offers picnic houses for BBQ. They also do medical and SPA service: massages, saunas,etc. It's a good choice to rent a room in a hotel near the sea for the price of renting apartment in the city center.
See also: Kiev apartments for rent.
Discovery hotel (motel) 1700.00 RUB
28 doubles for 1'700 RUB, big TV, DVD in rooms. Free Wi-Fi zone, restaurant and several types of saunas and "banyas" (800 RUB/h).
Some hotel descriptions claim that it is located in the center. I wouldn't say so - it's about 10 minutes driving by car to the city center without traffic jams and upto 30 with one, not so comfy for travellers w/o car. But still - quite good and cheap option.
Update March 2010:People report, that the hotel do not want to deal with foreigners if they stay for a short period of time.