It seems like it is different with every program. A lot of them don't use or require IQ scores b/c most kids don't have them and it is too expensive for the schools to test themselves. Although, they often will accept IQ scores if you have them. I do know a few that won't take outside scores, though, and only consider scores obtained by the schools.
The factors usually used are achievement scores, scales filled out by teachers and/or parents, and sometimes group ability test scores like the OLSAT, Raven, CogAT, etc. Depending on what the program is, they may look at composite scores or subject specific scores. Most of the GT programs I've seen where I live fall into two categories:
1) subject specific program like a reading GT class;
2) pull out where they do things like critical thinking puzzles.
For the first type of program, the scores that would count would be the verbal subtest on something like an IQ or CogAT, reading and writing achievement scores (or math/quantitative if it was a math pull out)
For the second, they tend to look more at rating scales of personality traits and/or composite scores on ability or achievement tests.