What pauper cards are legal in paper but not MTGO
According to Wikipedia, all sets since (and including) "Invasion" have been released on MTGO. This means the Masques, Urza, Tempest, Mirage, (most of) Ice Age, and Homelands blocks are not included in MTGO. In addition, core sets up until 6th edition and the Alpha, Beta, Unlimited, Arabian Nights, Antiquities, Revised, Legends, The Dark, and Fallen Empires expansions are also excluded from MTGO.

Rather than searching gatherer for these sets, it is better to exclude the sets that are in MTGO, because that will exclude cards from early sets that got re-printed in later sets.

As of the release of Magic Origins, the following gatherer search should provide a list of all commons that were only printed in the sets before MTGO was released.

shortened url: http://goo.gl/O8OdKM

full url:

http://gatherer.wizards.com/Pages/Search/Default.aspx?action=advanced&amp;set=+![%22Magic%20Origins%22]+![%22Seventh%20Edition%22]+![%22Eighth%20Edition%22]+![%22Ninth%20Edition%22]+![%22Tenth%20Edition%22]+![%22Magic%202010%22]+![%22Magic%202011%22]+![%22Magic%202012%22]+![%22Magic%202013%22]+![%22Magic%202014%20Core%20Set%22]+![%22Magic%202015%20Core%20Set%22]+![%22Invasion%22]+![%22Planeshift%22]+![%22Apocalypse%22]+![%22Odyssey%22]+![%22Torment%22]+![%22Judgment%22]+![%22Onslaught%22]+![%22Legions%22]+![%22Scourge%22]+![%22Mirrodin%22]+![%22Darksteel%22]+![%22Fifth%20Dawn%22]+![%22Champions%20of%20Kamigawa%22]+![%22Betrayers%20of%20Kamigawa%22]+![%22Saviors%20of%20Kamigawa%22]+![%22Ravnica:%20City%20of%20Guilds%22]+![%22Guildpact%22]+![%22Coldsnap%22]+![%22Time%20Spiral%22]+![%22Planar%20Chaos%22]+![%22Future%20Sight%22]+![%22Lorwyn%22]+![%22Morningtide%22]+![%22Shadowmoor%22]+![%22Eventide%22]+![%22Shards%20of%20Alara%22]+![%22Conflux%22]+![%22Alara%20Reborn%22]+![%22Zendikar%22]+![%22Worldwake%22]+![%22Rise%20of%20the%20Eldrazi%22]+![%22Scars%20of%20Mirrodin%22]+![%22Mirrodin%20Besieged%22]+![%22New%20Phyrexia%22]+![%22Innistrad%22]+![%22Dark%20Ascension%22]+![%22Avacyn%20Restored%22]+![%22Return%20to%20Ravnica%22]+![%22Gatecrash%22]+![%22Dragon%27s%20Maze%22]+![%22theros%22]+![%22Born%20of%20the%20Gods%22]+![%22Journey%20into%20Nyx%22]+![%22Khans%20of%20Tarkir%22]+![%22Fate%20Reforged%22]+![%22Dragons%20of%20Tarkir%22]&amp;rarity=+[C]




Edit: Looking at the results, it looks like the query wasn't perfect. But it's a good start.