Liebeck & Saxl (1986) classified the ones whose socle is a simple exceptional or sporadic group.
Examples
If G is any 4-transitive group acting on a set S, then its action on pairs of elements of S is a rank 3 permutation group.[1] In particular most of the alternating groups, symmetric groups, and Mathieu groups have 4-transitive actions, and so can be made into rank 3 permutation groups.
The projective general linear group acting on lines in a projective space of dimension at least 3 is a rank-3 permutation group.
Several 3-transposition groups are rank-3 permutation groups (in the action on transpositions).
It is common for the point-stabilizer of a rank-3 permutation group acting on one of the orbits to be a rank-3 permutation group. This gives several "chains" of rank-3 permutation groups, such as the Suzuki chain and the chain ending with the Fischer groups.
Some unusual rank-3 permutation groups (many from (Liebeck & Saxl 1986)) are listed below.
For each row in the table below, in the grid in the column marked "size", the number to the left of the equal sign is the degree of the permutation group for the permutation group mentioned in the row. In the grid, the sum to the right of the equal sign shows the lengths of the three orbits of the stabilizer of a point of the permutation group. For example, the expression 15 = 1+6+8 in the first row of the table under the heading means that the permutation group for the first row has degree 15, and the lengths of three orbits of the stabilizer of a point of the permutation group are 1, 6 and 8 respectively.
Group
Point stabilizer
size
Comments
A6 = L2(9) = Sp4(2)' = M10'
S4
15 = 1+6+8
Pairs of points, or sets of 3 blocks of 2, in the 6-point permutation representation; two classes
A9
L2(8):3
120 = 1+56+63
Projective line P1(8); two classes
A10
(A5×A5):4
126 = 1+25+100
Sets of 2 blocks of 5 in the natural 10-point permutation representation
The Chevalley group of type G2 acting on the octonion algebra over GF(2)
Ω7(3)
G2(3)
1080 = 1+351+728
The Chevalley group of type G2 acting on the imaginary octonions of the octonion algebra over GF(3); two classes
U6(2)
U4(3):22
1408 = 1+567+840
The point stabilizer is the image of the linear representation resulting from "bringing down" the complex representation of Mitchell's group (a complex reflection group) modulo 2; three classes
^The three orbits are: the fixed pair itself; those pairs having one element in common with the fixed pair; and those pairs having no element in common with the fixed pair.
References
Bannai, Eiichi (1971–72), "Maximal subgroups of low rank of finite symmetric and alternating groups", Journal of the Faculty of Science. University of Tokyo. Section IA. Mathematics, 18: 475–486, ISSN0040-8980, MR0357559
Brouwer, A. E.; Cohen, A. M.; Neumaier, Arnold (1989), Distance-regular graphs, Ergebnisse der Mathematik und ihrer Grenzgebiete (3) [Results in Mathematics and Related Areas (3)], vol. 18, Berlin, New York: Springer-Verlag, ISBN978-3-540-50619-5, MR1002568