Off the top of my head, the current official optional/variant rules I use are:
-Multiclassing (discouraged though)
-Feats
-Skills with alternate ability scores
-Healer's kit dependency for short rest healing
-Slower natural healing (the one where you regain half HD but no hit points on a long rest)
-Combat Options: Climbing onto a bigger creature, Disarm, Overrun, Tumble, Shove Aside
-Technically Lingering Injuries (since it doesn't give you solid rules for when to make the roll, I came up with my own, and tweaked the permanence of the injuries), but it came up so rarely with my rules that it's only happened once in hundreds of hours of play (probably should have happened more but I don't remember to use it)
-NPC mob rules
-Automatic success on skill checks--but I tweaked this one to only apply if you are proficient
I used the variant Encumbrance rule (rather than the standard Carrying Capacity rule) at the start of my long campaign to make things a little grittier at level 1, and then switched to Carrying Capacity. This was actually a planned thing, rather than a change of mind.
There may be one or two more I'd find if I went through the books looking.