"Effect" is a general term that encompasses everything that a card does except for doing actual damage.
"Special Conditions" are a special subset of effects that all follow certain rules together, such as shutting down most (not all!) Pokemon Powers.
Special Conditions include the following effects:
Asleep
Confused
Paralyzed
Poisoned
Burned
The details of Special Conditions are outlined in detail in all rule books, so I won't repeat them here.
Best to get a rule book, for this and many other reasons.