The ionization of H-2, D-2, and HD molecules by metastable neon atom collisions is studied in a crossed beam experiment. The relative total ionization cross sections and the product branching ratios have been measured as a function of the collision energy in the laboratory range 0.04-0.3 eV. Penning (H-2(+), D-2(+), and HD+), associative (NeH2+, NeD2+, and NeHD+) and rearrangement (NeH+ and NeD+) ionization occur in all the three isotopic variants, Penning ionization being the dominant channel. For the rearrangement it is observed that NeD+ is produced with more efficiency than NeH+. In the case of Ne*-HD, an NeD+/NeH+ branching ratio of similar to 1.5 is observed. This ratio is below the statistical expectation for the isotope effect. The total ionization cross sections are analyzed in terms of an optical potential. The opacity function, provided by this potential, is then used for a first approach to the description of the collisional auto-ionization dynamics through a two step model.