Alistar is a tanky support that is especially aggressive during the early lane phase. However his aggression and ability to sustain this aggression depends entirely on his cooldown and mana regeneration. So these are the two areas that should be focused on with runes.
For Marks use defense marks. As a support, the main opposing damage should come in the form of physical attacks from the enemy AD carry. You don't really want to take anything offensive since as a support Alistar, dealing damage is not your job.
For Seals, I strongly suggest flat mana regeneration. You want to get flat mana regeneration because you want to optimize early game stats. Late game, Alistar has a lot less trouble with mana control.
For glyphs, focus on flat cool down reduction. Alistars main role in to essentially CC the enemy to protect your carry or to serve the enemy on a platter for your carry. Alistar's effectiveness is dependant on how quickly/often Alistar can do this.
For quintessences I would recommend health quintessences. If these are not available to you, then either additional cooldown reduction or mana renegeration will be great on Alistar.
Although these runes are flat stats instead of per level, it will still scale well into late game because Alistar should have no problem with mana in late game. As for cool down reduction, there are many support items that offer cool down reduction. In late game, you will achieve the max 40% cooldown without having the scaling cooldown reduction runes, if you build correctly (Revelry and Zeke's will put you at about 40%).