To list the most commonly cited reasons:
Usability:
Framed pages can be problematic to "bookmark" as a user
Some browsers (including some emerging web tv or supermarket access type services) do not support them
The use of frames (at the most basic level) changes the way a user interacts with a site (ie moved / oddly placed scroll bars).
Being seen:
Search engines....arrrgh. Unless you code smart, you could have search engines giving priority to one of the pages you have appearing in a frame. If all you navigation is in a seperate frame, you have users hitting a dead end.
Similarly, totally useless (on their own) frames could be indexed.
Frames can be used really nicely for effect (for a good example see
www.kvetch.com), but be warned, the pitfalls are many!
H