For Commander Protection, I sometimes use [card]General's Kabuto[/card] as prevents combat damage as well.
Dolmen Gate is also great for keeping your commander around after combat. [card]Rogue's Passage[/card] is also great way to make your commander go through repeatably.
Kusari-Gama +
Grappling Hook is really good at wiping an opponents board. It can target a weak creature and kill the big ones that may have hexproof or Shroud.
I found
Evangelize in my Binder and thought it would be worth a try. It is expensive, but late game use is just life saving. Steel that Vorinclax, that commander with an arsenal of equipment, Their combo enabler, or whatever looks good. Buyback is what I really abuse.
Grafted Exoskeleton is
fun with unblockable creatures.
Spore Frog +
Genesis or
Nim Deathmantle is great stopping attacking.
Crib Swap (another remove from game spell), [card]Hero's Demise[/card] (cheap commander killer),
Evacuation (anti
Rude Awakening),
Pentarch Paladin (white destroy target permanent) , and
Ertai, Wizard Adept (repeatable counter spell ability, found it in a $1 bin) are removal spells I rarely see in opponents decks. I found them quite effective as there is limited numbers of great removal against certain strategies.
Lastly, I found
Prahv, Spires of Order to be a great damage stopper. It gets around hexproof or Shroud creatures attacking you. It also stops huge burn. I have survived games with it.