For my low-magic games, I use:
Combat, weapons mechanics & / or damage- use lowered MDT dependent on size, Con mod, natural armor, and Fort save.
Combat, AC versus defensive roll / damage absorption- use level and class based AC bonus
Spell System / magic system (higher or lower or totally different)- lower magic, and completely different classes. No bards, wizards or sorcerers; new spell levels gained every 3 levels rather than every two, spellcasting rolls, etc.
Alignment- only outsiders, some undead, and inherently supernatural creatures show up on the Detect spells, and only those critters are affected by any spells that specificy they affect and alignment type.
Classes or Races- Only humans as race, although there are 14 different cultures that are effectively different "races" in D&D terms. 6 new arcane casters, 1 new divine caster, and 1 spiritual caster (the witch).
Experience Points / Leveling- None of that CR/EL crap- I level the group after an appropriate period of time.
Skills/Character Generation- I use social class tables for character generation that take into account a few extra skill points based upon background. Its semi-random, but the players have some control too.