For Bachelors in Engineering:
NUST, Karachi, Islamabad, Rawalpindi, Risalpur (Isloo branch is probably the best engineering uni in Pakistan as far as my friends tell me).
NED, Karachi (Pros: supports amazingly large number of engineering subjects, has state of the art devices to help students learn, awesome teachers especially in 3rd and 4th years, super fast computers (i5) and very fast speed campus wide internet, very competitive environment. Cons: Architecture in old departments is poor, no air conditioning, not well made auditoriums for the Electrical, Civil and Mechanical departments [other departments have awesome auditoriums and 5 star buildings].)
GIKI, KPK (very tough to get into, but is awesome as per my 2 friends who are studying there).
UET, Taxila (have heard great things about this university).
Karachi University, Karachi (publishes huge number of research papers each year, provides engineering in almost every single subject).
Sir Syed University Of Engineering And Technology (have heard good things about this place, but there is so much politics here).