As you can see from the replies above, there are various reasons to do missions for any particular NPC corp.
Missions will reward you with:
- standings towards the corp
- Loyalty Points (LP) - which you can use in the corp’s LP store to buy things, typically to re-sell for ISK.
As mentioned above, standings with the corp just unlock higher level agents from the same corp for you. Exception is that the Jita trade hub is at the Caldari Navy 4-4 station, and so if you build standings with Caldari Navy you’ll get a slight reduction in taxes at Jita. Currently, people use citadels to bypass taxes, and there are several player-owned citadels that offer low taxes for the general public. Incidentally, similarly to Jita being in a Caldari Navy station, the second-busiest trade hub, Dodixie, is in a (Gallente) Federation Navy station.
Otherwise it’s all about the items offered in the loyalty point stores. Most corps offer generic items - implants, basic ships. Sisters of EVE offers their (very nice) SoE probes and probe launchers, as well as the SoE exploration ships. So for the effort that you put in to get LP’s from missions, the SoE store has nice things that you can re-sell for ISK. Unfortunately, most of the SoE agents are distribution (hauling) agents, not security (combat).
To help you figure out which LP stores are better:
Ellatha’s LP Store Database is sorted by each Empire and each corporation, so you can browse.
Steve Ronuken’s Fuzzwork Database (linked above by Chainsaw Plankton) lets you see how much ISK you can get for any particular item. Click the blue button then pick your NPC corp to look at what’s profitable and what’s not.