Personally, I don't usually devote card slots specifically to protecting my commander. I also think that
Lightning Greaves and
Swiftfoot Boots are largely overplayed precisely because people are overly afraid of their commander (and their stuff in general) being targeted. Of course, the fact that they are overplayed doesn't mean that they are bad: they are actually some of the best equipments in (casual) EDH if you can take advantage of the haste ability.
Sure, your commander can die, but you can cast it again. In many decks, my plan to "protect" my commander is just to have enough mana to cast it again as many times as needed. I also value graveyard recursion highly, and sometimes you can just let your commander go to the yard and
reanimate it later. These are just some example of ways to "protect" your commander without actually devoting card slots to this.
The best way to protect a commander also depends on the specific synergies of the deck. For example,
Stubborn Denial is amazing with commanders with power 4 or greater, and
Heroic Intervention or
Flawless Maneuver are ideal for decks that tend to amass large boardstates. And as mentioned by MustaKotka, counterspells are great to pretect your commander because they can be used to stop other threats.
All that said, if I had a commander that I wanted to protect at all costs, without knowing anything about specific synergies or the colors of the deck, I would still choose
Lightning Greaves*. Overplayed, yes, but still an excellent card
(*) Unless of course I'm playing Voltron or something similar: I want to be able to target my commander in that case!