Ok, I've thought about these various situations quite a lot and I would like to hear your views; assume you have some papers from proceedings and journals:

Situation 1a:
All papers have been published in a nonindexed proceedings/journals and not peer-reviewed. No one has cited your paper or it has been cited by 5-6 people only. The papers have a mixture of you as a first author and co-authors

Situation 2a:
All papers have a mixture of peer-reviewed and indexed and nonindexed proceedings/journals but most of your cited papers have been cited by you only. The papers have a mixture of you as a first author and co-authors

Situation 3a:
Same as situation 1a, but you are the first author for most of the papers.

Situation 4a:
Same as situation 2a, but you are the first author for most of the papers.

Situation 5a:
You only have nonindexed nonpeer-reviewed proceeding publications

For the 5 situations, which one will put you in a bad (as well as good maybe) position in terms of job prospects?
I was thinking about this as I'm getting increasingly worried about publications and job prospects : (

Another completely different situation:

Situation 1b:
No publications but have a PhD.

Situation 2b:
Some good publications but have only a Masters.

Which one is more promising?

Always aim for (i) peer review and preferably (ii) indexed. Don't worry so much about citations - that can always develop over time. I don't think anyone would judge an early career researcher adversely if their research had yet to be cited, but they might query the quality of work if it wasn't peer reviewed.

At this stage, if you come out of your PhD with a couple of first/second author peer reviewed publications, you're doing well. Conference proceedings (even if indexed) are generally less important, though that can vary by field. Which field/discipline are you in?

As for your second scenario comparison, PhD vs publications and MSc, it depends entirely what job you'd be going for.

You should really focus on the quality of your papers.

Anyway, impact factor is also very important. Below are some examples...
1. Journal of Computational and Applied Mathematics (JCAM) (ISI impact factor: 1.048 (2008), 5-Year Impact Factor: 1.138)
2. Computers and Mathematics with Applications (CMA) (ISI impact factor: 0.997 (2008), 5-Year Impact Factor: 1.049)
3. Applied Mathematics and Computation (AMC) (ISI impact factor: 0.961 (2008), 5-Year Impact Factor: 1.124)

Better still, it depends on the co-authors: Nobel laureate, Field medalist, Director, Head of Department...
Or many different groups of researchers; it shows that you can work with anyone.