Ysmault is off limits because it is where the Five Inversions are imprisioned (and their followers). The Five Inversions only goal is the erradication of life in the universe, and because their planet was destroyed by the Manhunters, which were created by the Oans, they hate the Oans above all else. The planet is forbidden to all so they don't have an opporuntity to escape (which happens when Abin Sur goes there).
Sector 3601, which is technically part of the Unknown Sectors since it is not within the 3600 protected by the Lattern Corps, is off limits so as not to provoke the Manhunters.
In addition, the Manhunters turned the desolate planet of Biot in Space Sector 3601 as their new homeworld which was part of the Unknown Sectors. This combined with the fact that the Guardians did not wish to provoke the Manhunters meant that it was left abandoned and isolated from interference by the Green Lanterns.
The Unknown Sectors:
According to the Guardians, the reasons for the formation of the Unknown Sectors was because of chaotic events as well as time constraints which prevented them from being organized.
As a place where Lanterns didn't go it became a breeding ground for the seedy characters of the universe. It did not remain permanently off limits though.
To [Guy Gardner's] surprise, the Oans agreed with him that this juncture of time required their presence to be felt in the Unknown Sectors. Thus, they authorised him to be sent into an expedition into the Unknown Sectors which would allow Gardner to secretly fulfil the pact he made with the Red Lantern Corps leader. Later joined by Kilowog, Arisia and the Red Lantern Bleez; Gardner formed the Emerald Warriors with Guy going on a secret mission to combat the menace stirring in the Unknown Sectors.