(in approximately chronological order)
Allen E. Hatcher, The second obstruction for pseudo-isotopies. Bull. Amer. Math. Soc. 78 (1972), 1005-1008.
Allen Hatcher and John Wagoner, Pseudo-isotopies of compact manifolds. Astérisque, No. 6. Société Mathématique de France, Paris, 1973. 275 pp.
Allen E. Hatcher, Concordance and isotopy of smooth embeddings in low codimensions. Invent. Math. 21 (1973), 223-232.
Allen E. Hatcher, Parametrized h-cobordism theory. Ann. Inst. Fourier (Grenoble) 23 (1973), 61-74.
Allen E. Hatcher, Pseudo-isotopy and K_2. Lecture Notes in Math., Vol. 342, pp. 328-336, Springer, Berlin, 1973.
Allen Hatcher and Frank Quinn, Bordism invariants of intersections of submanifolds. Trans. Amer. Math. Soc. 200 (1974), 327-344.
A. E. Hatcher, Higher simple homotopy theory. Ann. of Math. 102 (1975), 101-137.
Allen Hatcher and Terry Lawson, Stability theorems for "concordance implies isotopy" and "h-cobordism implies diffeomorphism". Duke Math. J. 43 (1976), 555-560.
Allen Hatcher, Homeomorphisms of sufficiently large P^2-irreducible 3-manifolds. Topology 15 (1976), 343-347.
A. E. Hatcher, Concordance spaces, higher simple-homotopy theory, and applications. Proc. Sympos. Pure Math., XXXII, Part 1, pp. 3-21, Amer. Math. Soc., Providence, R.I., 1978.
A. E. Hatcher, Linearization in 3-dimensional topology. Proceedings of the International Congress of Mathematicians (Helsinki, 1978), pp. 463-468, Acad. Sci. Fennica, Helsinki, 1980.
A. Hatcher and W. Thurston, A presentation for the mapping class group of a closed orientable surface. Topology 19 (1980), 221-237.
A. Hatcher, On the diffeomorphism group of S^1 x S^2. Proc. Amer. Math. Soc. 83 (1981), 427-430.
W. Floyd and A. Hatcher, Incompressible surfaces in punctured-torus bundles. Topology Appl. 13 (1982), 263-282.
A. E. Hatcher, On the boundary curves of incompressible surfaces. Pacific J. Math. 99 (1982), 373-377.
Allen E. Hatcher, A proof of the Smale conjecture. Ann. of Math. 117 (1983), 553-607.
Allen Hatcher, Hyperbolic structures of arithmetic type on some link complements. J. London Math. Soc. (2) 27 (1983), 345-355.
A. Hatcher and W. Thurston, Incompressible surfaces in 2-bridge knot complements. Invent. Math. 79 (1985), 225-246.
W. Floyd and A. Hatcher, The space of incompressible surfaces in a 2-bridge link complement. Trans. Amer. Math. Soc. 305 (1988), 575-599.
A. E. Hatcher, Measured lamination spaces for surfaces from the topological viewpoint. Topology Appl. 30 (1988), 63-88.
A. Hatcher and U. Oertel, Boundary slopes for Montesinos knots. Topology 28 (1989) 453-480.
Allen Hatcher and Darryl McCullough, Finite presentation of 3-manifold mapping class groups. Lecture Notes in Math., 1425, pp. 48-57, Springer, Berlin, 1990.
Allen Hatcher, On triangulations of surfaces. Topology Appl. 40 (1991) 189-194.
A. Hatcher and U. Oertel, Affine lamination spaces for surfaces. Pacific J. Math. 154 (1992), 87-101.
Allen Hatcher, Some examples of essential laminations in 3-manifolds. Ann. Inst. Fourier (Grenoble) 42 (1992), 313-325.
Allen Hatcher, Homological stability for automorphism groups of free groups. Comment. Math. Helv. 70 (1995), 39-62.
A. Hatcher and U. Oertel, Full laminations in 3-manifolds. Math. Proc. Cambridge Philos. Soc. 119 (1996), 73-82.
Allen Hatcher and Karen Vogtmann, Isoperimetric inequalities for automorphism groups of free groups. Pacific J. Math. 173 (1996), 425-441.
Allen Hatcher and Darryl McCullough, Finiteness of classifying spaces of relative diffeomorphism groups of 3-manifolds. Geometry and Topology 1 (1997), 91-109.
Allen Hatcher and Karen Vogtmann, The complex of free factors of a free group, Oxford Quarterly 49 (1998), 459-468.
Allen Hatcher and Karen Vogtmann, Cerf theory for graphs, J. London Math. Soc. 58 (1998), 633-655.
Allen Hatcher and Karen Vogtmann, Rational homology of Aut(F_n), Math. Research Letters 5 (1998), 759-780.
Allen Hatcher, Pierre Lochak, and Leila Schneps, On the Teichmüller tower of mapping class groups, J. reine angew. Math. 521 (2000), 1-24.
Allen Hatcher and Karen Vogtmann, Homology stability for outer automorphism groups of free groups, Algebraic and Geometric Topology 4 (2004), 1253-1272. Erratum: AGT 6 (2006) 573-579, with Nathalie Wahl as a third author.
Allen Hatcher and Nathalie Wahl, Stabilization for the automorphisms of free groups with boundaries, Geometry and Topology 9 (2005), 1295-1336. Erratum: GT 12 (2008) 639–641.