Here are the answers to your questions.

1) How can one with a B permit and earning less than 120k check if it is worthwile doing a tax return? I checked the online calculator of the national web site but the results are strange. When you add up the kanton and bundes tax for my Kanton and Gemeinde, the numbers are much higher than the total listed at the bottom. This also happens for other kantons (try Zug).

The first thing you need to be aware of is exactly what your taxable income is. Then you can use tables provided by your kantonal steueramt to do the calculations. Try the website they are usually pretty good.
The calculators that you find online will only every give a good estimate and are really for comparison purposes. There is so much that they do not ask that their use is limited. Calculating your taxable income is straightforward for Quellensteuer - you take the monthly income plus the PK contributions multiply by 12 add any bonus and there you have it. When you are thinking of doing a tax return ie a formal one then go into the local Gemeinde and ask for the tax return forms. Alternatively Bern might have software that will do it for you - check. Then you need to carefully fill in the amounts in the respective boxes and check then your taxable income at the end. Note if it is here more then it is not worth doing.

Also, my tax is complicated as I pay employer contributions as well, so would I even be able to pre-calculate whether it is worth submitting a tax form? (I work for the EU, which means my Swiss employer is lucky as I pay everything).

Yes this is a typical contractor situation and it is very possible as the employer contributions do not vary, well they almost don't...

2) Has anyone here had to pay more after you tried to claim tax back in the B permit, less than 120k situation?

The question is really is it possible and the answer is very definitely yes!

3) My gross salary is 76000 (I am researcher) but my pension is only calculated on the basis of 48000. Is this normal? (It says my salary is only insured at a fraction of my net salary). Should I worry about this?

If you are paying quellensteuer and based on a gross salary of 76K no not really. The actual contribution amounts for the pension fund are not fixed by law. There is a minimum and a maximum but other than that they are free to vary. The primary consideration is that the pension fund is taxable with only 7% but if you are paying quellensteuer this is anyway irrelevant.

4) If a person has to pay quellensteuer, is it still useful to create a 3a pillar? I.e., is it worth opening a Fisca account? I guess people with a C permit can deduct their 3a payments, but how does this work with quellensteuer? Can one indicate how much you put in and then get a reduction the next year of your quellensteuer??

No and No are the answers here. Please be aware that it is not simply C permits and the rest. Anyone can complete a tax return and be taxed normally in which case this would come into play.

5) I live in Bern and pay about 31% to taxes and insurances. Would you say this is average, better or worse than normal?
Based on your salary I would say you are paying far too much in the way of insurance. Your taxable portion should not exceed 23%. IF it does then there is something wrong.

6) Is it common for the 13th month to be taxed as much as the other 12months? My statement treats it equally (taxes are deduced based on 13 months of equal income). IS this normal?[/quote]

This is permissable but not normal. It is useful for quellensteuer payers but you might find yourself receiving a bill if you leave shortly after receiving the 13 month unless it is paid in arreers.

Any questions post away