This is a tricky question to answer without a better idea of what your overall aims are, because it's those that will decide which faction and which agents you should do mission running for.
In general, when you run missions for a faction you'll be improving your standings for that faction (and its allies) and reducing your standings for the opponents of that faction (and perhaps their allies). By avoiding the "blow up ships of this faction" mission types, you can really reduce the amount that your standings go down with opposing factions, but there will always be a slow general decline.
So this question (in essence) seems to boil down to "which faction should I aim to improve my standings with?". The answer to that one should be "the faction you want to do R&D with". Reason being; all mission rewards can be considered more-or-less equal, but faction standings give you a solid base for R&D corp standing which can be improved by running missions for that corp which then gives you a really nice standing with their R&D agents.
What if you don't entirely understand R&D agents? No idea why they seem to be my main point? Here you go: http://wiki.eveonline.com/en/wiki/Research_agent
The reason I would call this (standing with R&D agents) the most important thing to develop via mission running is because there's no other way to get it and because it's so valuable to have. R&D agents are pretty much synonymous with "free ISK", so the value is right there. Are you not working towards R&D agents? Why not? Is there something else you're working towards? Like a certain item reward or BPC from the mission rewards store? Well then, run the missions that will get you there. If you don't have any kind of a long-term goal with your mission running (trying to get high faction standings so you can launch a POS? Want to have an empire jump clone?) then congratulations, now you've got one: Develop R&D Agents for income purposes! Find which R&D agents are available in your local hangout (or the portion of empire space you visit most often, even if it's only once a year that's fine) and work towards them. Not sure which of the many available R&D agents are best? Check out the current market value of the Datacores they produce, go for the most valuable one(s).
As with most things in EVE, 'what way should I do it?' questions are always answerable with 'well, what's your goal?'.