Here are some of my pet cards for Commander that one might consider underplayed. With little exception, these cards are archetype neutral and see play in all of my decks which have the colors for them, but are at 3% or lower on EDHREC (and in my playgroup).

Garruk Wildspeaker is a personal favorite, my first ever planeswalker. Coming down on four cmc, he can untap two lands every turn. Garruk is a serious piece of ramp in green and one of the few ramp cards I would pay four for (also Skyshroud Claim and Explosive Vegetation). I usually use his uptick ability nonstop throughout the game until I decide to use his ultimate, the well-known Overrun effect. Overrun is a powerhouse in commander already, buy Garruk lets you have two in your deck! The value here is great without being game-warping enough to paint a target on your back. He also has a middle ability which can help you protect him or give a boost to your creature tokens build.

Chandra, Flamecaller finds her way into most of my Red decks due to that incredible middle ability, refilling my hand when I need it. Her top ability provides some attackers and/or sac fodder to the board, and the bottom ability wipes all the weenies off the board. This is a versatile walker that really lives up to its casting cost in my opinion, and can be as flexible and powerful as any big modal spell (Fiery Confluence and Incendiary Command being the red ones).

Seals - There are two key reasons I would pick a seal over other removal at the same price. First, they save mana during key turns by coming down early on turns one or two if they're in your opening hand. After that, they will be available on turns where you otherwise had to tap out to play your general or ramp into the late game. Putting them down on early turns also makes them far less likely targets for countermagic. Second, the seals act as rattlesnakes on the board, giving you a key bargaining chip when opponents are deciding who to mess with. Throw out your unsummons, disenchants, and naturalizes for these three gems already. The tertiary boon is enchantment synergy, though this will vary deck to deck. Certainly some decks would rather have instants and sorceries, though I think enchantress decks are just as if not more common. Of all the seals printed so far (there are six) the three I use most often in EDH are Cleansing, Primordium and Removal, but I think Doom and Strength may be good in the right deck. Sadly, I doubt Seal of Fire would ever be powerful enough to make the cut (but it's great in my cube).

Oblation is a forgotten staple which used to be found in many EDH decks before the command zone rules changed. Despite this, the card is still very powerful in a color that will take all the spot removal it can get. Unlike its younger cousin Chaos Warp, however, Oblation also makes a decent target-yourself card. Where warp flips one card off the top and misses non-permanents, Oblation simply draws two. This is very welcome in mono-white (and white-red and white-green), where I have Oblated my own lands with no other cards in hand. Just as good, I can oblate a permanent of mine that an opponent is targeting to keep it out of the grave and refill my hand.

Llanowar Druid - Does your deck want big combos, big creatures, X cost spells, or big turns? Does your deck contain forests? If you answered yes to one-and-a-half or more of these questions, your deck might want Llanowar Druid.