Great job or great organization?

I'd take Job 2 without hesitation. There is always room for a job to change and become more interesting. And work/life balance is unbelievably important. There's usually no fixing a crap organization. The issues you're finding now after only 6 months are very possibly just the tip of the iceburg.

I would go with the healthy organization. Working in a sick system will give you bad habits, and you will be powerless to change the dynamic. Also, jobs that are frustrating but fun when you're working part time can feel a lot more frustrating and a lot less fun when you take them on full time. But definitely be looking for new opportunities in the good organization! If they are really that good they should support your professional growth as well as your work in your current position.

I've had jobs from cleaning hospitals to working "big and important" jobs for international corporations, and the #1 lesson I've learned, & keep re-learning, is that the people with whom you work have the biggest impact on how happy your job is. A yucky, non-challenging job with great co-workers and a healthy organization is (in my experience) way better than a wonderful job with awful to okay co-workers and a rotting core. #2 is the less commute I have, the happier I am. (Think about this way: a half hour commute each way - an hour a day total - is 40 hours a month...the equivalent of 1 work week a month just driving your car.) But it's not just me; there's several studies that support how commuting time affects lifestyle and happiness. (It's also more time sitting, and sitting time has big, long-term adverse affects on health.) As someone pointed out already, the question you have to ask yourself is what do you value most, and what are you willing to give up for that value? You can easily have some impact on your simple job and its responsibilities. It's incredibly difficult to change company culture.

In a similar situation, I left "Job 2" for "Job 1" and it was HANDS DOWN the best career decision I've ever made. While there are millions of bad things about working for poorly run organizations, some of the good things (like you pointed out), like being able to have way more responsibility or flexibility than you would have in a more well-run organization can do wonders for you at the early stage of your career if you take advantage of the unique opportunities present in the chaos. I stayed at my version of "Job 1" for three years, and while I was there, I volunteered to lead or develop the stuff that no one else wanted or had time to do and got a TON of experience. Now I have a job at a super stable, respectable organization, but it's at a much higher level. It would have taken me 10+ years to "work my way up" in a stable organization. So I'd go for "Job 1". Don't stay forever, but use it to make yourself the best possible candidate for "Job 3" in a year or two.

I commented once but want to comment again about the risks of taking an admin job hoping it will turn into a program job. I would've been more optimistic about this (it sounds good in theory), but at my last job, I saw two people leave an admin job because their hopes to transition into work they would find more meaningful hadn't come to pass. You need to be climbing the right ladder, developing the right skills, gaining experience that's applicable -- not trying to learn by osmosis. The fact that Job #2 is well run is all the more reason to think you won't do much program work (unless you are officially, say, half-time admin, half-time program). Unless they'll give you a formal commitment on this, I wouldn't do it. It's true that you don't want to be affiliated with Job #1 forever, lest its bad reputation rub off on you. But the flip side of that coin is that people are not surprised to see staff leaving those organizations after a relatively short time. There are certain organizations in my field from which you regularly see refugees (for lack of a less dramatic word). "Oh yes, another person who used that job to get their foot in the door but who has too much talent and self respect to stay long." Will you have an opportunity to build up relationships outside of the organization via partnerships with other groups, monthly professional development gatherings of the "XYZers of Chicago," etc.?

job 1 is primarily programming-oriented, and job 2 is primarily administrative, so these are two very different career paths. This is an important clarification. Especially in an organization like Job 2, the wall between Operations and Programs is not that permeable. People advance within their own team but don't often cross over. See if Job 2 would give you some assurances about your ability to switch to a program-side job if one arose (assuming you performed well). Unless the assurances feel solid, I'd decline Job 2 in the most gracious way possible, take Job 1, and then apply when a relevant program-side job arose at the healthy [job 2] organization. Do not hunker down to stay at Job 1 for a long time. Keep your resume current and send it out when you see opportunities to transfer laterally to a better-run organization. You want to be learning from and associated with healthy organizations, both for your well-being and for your career.

If you're young & flexible (no kids), take job 1 but keep looking. Office/admin work can become a pink-collar yoke. Have stuff on your resume that you want to keep doing.

I don't see that there's a great answer either way -- I'm somewhat inclined to say take job #1 with an exit strategy because I agree with salvia and the young rope-rider, but getting a new job is still easier said than done in this economy. If things turn awful at job #1, that's going to suck your will to deal with a job search, plus you'll have less time for that job search since you'll have a longer commute. Also, if you're doing good programming, but at an organization that is known to be a mess generally, that complicates how your experience will be perceived by future employers. If you think that job #1 will offer you the chance to be perceived externally as a rising star in your field, it might be worth the risk that your workplace will implode into an epic mess in some fashion. But if they're both entry-level jobs where your contributions will mostly be seen and appreciated in-house, job #2 sounds less risky.

Another vote for Job #2. I have found that - barring a job that is a really poor fit with one's temperament and skill-set - a humdrum job at a terrific organization with great co-workers and bosses is better than a job that looks good on paper, but the company culture is dysfunctional and/or your coworkers/bosses are toxic. A long commute is soul-sucking and a drain on your time and energy. People with long commutes are unhappier and unhealthier. Having no commute at all is a huge, huge perk. Work-life balance is another huge perk. "Terrific" jobs can sour quickly if accompanied by a toxic workplace, a long commute, or punishing hours. On the other hand, a "meh" job can be a great job if you like your co-workers, bosses, and workplace. And it's so nice to get home from work and have the time and energy to exercise, cook and socialize. If I had the choice, I'd jump on Job #2 and see if there was room for training and advancement there.