As you may have deduced, I am a neuroscience PhD student. I earned an undergraduate degree in neuroscience from Brandeis University, which is somewhat rare for having a neuroscience major and even rarer for allowing undergrads to earn a master's alongside their bachelor's degree (a dual BS/MS program, in my case). As such, my master's degree experience differed from a stand-alone MS program, but I was required to take graduate-level classes and to complete and defend a research thesis. This didn't seem too different from what my non-MS classmates were doing, to be honest. Many neuroscience classes at Brandeis contained undergraduate juniors and seniors in addition to first and second year graduate students, and neuroscience majors had the option to complete a research project and write a thesis to achieve departmental honors. The main difference was that I was required to take a set number of the upper level classes (all of which still contained undergrads) and I had to do an oral defense. Therefore, I feel that I would have been equally prepared, academically speaking, to go for my PhD even if I hadn't gotten my MS beforehand. I mainly did the BS/MS program because I had the time -- I attended summer school for a few years, so I had room in my schedule to take the extra classes without overloading any given semester. If I hadn't done the BS/MS I could have graduated early or triple majored (but Brandeis doesn't allow triple majors; I settled for two majors -- biology and neuroscience -- and a minor in classical studies).
When I got to my PhD program, I didn't find my classes to be significantly more difficult than the ones that upper level undergraduates take at Brandeis. I've only been here for one semester, of course, but my program at least is cognizant of the varying skill levels that students have in key subjects and has tried not to blow our minds too badly. We study a lot, but if unlike me you come into grad school with good study habits, you'll be okay. Of the 13 students in my PhD cohort, only two of us have an MS. Now, if my undergraduate performance had been worse (and it wasn't all that awesome to begin with, to be honest -- I graduated with a 3.4 GPA, which is good but not likely to wow anyone in and of itself), it might have been a good idea to apply to MS programs. An MS program (probably unfunded) would be more likely to accept a student with a borderline academic background and give them a chance. This, in turn, allows the student to make good grades and impress professors at the MS program, which helps them to be a more competitive PhD applicant if that is their eventual goal.
But, in my opinion, it is not necessary to apply for an MS if your goal is a PhD and you're just worried that you're not ready for graduate coursework. But what about research? Graduate school is primarily about research, and not all college students have the opportunity to do research at their undergraduate institution. If someone isn't sure whether he or she is any good at research, or likes doing research, or is allergic to latex gloves, should he or she start with the "baby step" of an MS program?
When I was getting my BS/MS, my advisors told me that I shouldn't expect the MS to make a big difference in getting into PhD programs. At the time, I wasn't sure that I even wanted to get a PhD, so I didn't take this into account. What does make a difference is research experience, and in the process of getting my MS, I got research experience. However, I also got research experience as an undergraduate research assistant before I started the BS/MS program, and as a laboratory technician after I graduated. I would argue that working as a lab tech is preferable to going for an unfunded MS, if your primary concern is getting research experience. A tech has to do a lot of lab drudgery, but this sort of job provides a dedicated research geek with the opportunity to work on independent projects and publish papers, if the PI is willing to support such endeavors. And unlike an unfunded MS, a lab tech job won't put you into debt.
I worked as a lab tech at Children's Hospital Boston for two years after graduating with my BS/MS. The job had its ups and downs, but I learned a lot about what it's like to be in the lab full time, which is how things are during the later years of a PhD program. I gained many new skills, and even got my name on a Science paper! (I was the least important author -- the last person before the list of collaborating PIs -- but hey, it counts for something, right?) When I applied to PhD programs, I was able to write intelligently about my research projects in my statement of purpose and provide a letter of recommendation from my PI. These things were far more important to the admissions committee than the MS degree on my CV.
So, my MS didn't contribute too much to my preparation for a PhD program. Did it help me get a job? Well... maybe. I did receive several offers when I was applying to lab tech positions in academia, industry, and at non-profit research hospitals. I'm not convinced that the MS is what impressed them, though -- I think I would have been a strong candidate without it, given my three years of undergraduate research experience, decent academic performance, and the fact that I interview well. When I came to Children's, I was the only tech I knew with a master's. I made the same salary as everyone else. Had I worked in industry, I probably could have qualified for a higher starting salary (say, Research Assistant II instead of Research Assistant I) and may have had more potential for advancement than someone with just a bachelor's, but I can't be certain as I didn't receive any formal offers from industry employers. (They took too long -- by the time one company wanted to set up a final interview, I had accepted the Children's job.) A friend who works in industry is currently getting his MS on the company's dime, slowly but surely, so some employers do value the degree and use it to determine candidacy for higher-level jobs.
After working as a tech, though, I decided I wanted to go back to school. I saw minimal potential for advancement, in terms of "creative control" and independence, if I didn't. I wanted the ability to set the direction of my research projects. And, I wanted more flexibility in my career choices. Not all PhDs become academics -- some work in industry, some work for institutions like the NIH, some go into law, some go into public policy, some take up science writing and/or publishing, and so on. People with their MS can do some of these things, but some preliminary research on the subject led me to believe that I'd have more options, and better options, if I got my PhD. This may not be the ideal path for everyone, of course. Some people become research specialists and spend their lives at the bench, using their expert skills and not stressing out over where the lab's funding will come from, and they love it. Being promoted above a certain level in science usually leads to detachment from the day-to-day routine of pipetting and centrifuging, which can be sad for people who have great hands for research and not-so-great heads for bureaucracy.
Therefore, I would advise any potential graduate student in the life sciences to consider what it is that they want out of their career. Meet different kinds of scientists and see if their jobs appeal to you, then figure out how to get those jobs. Working in your field for a while between undergrad and graduate school can be a great way to meet these people and figure this stuff out, in addition to making you a better candidate if you decide to apply to schools. Learn what you like and don't like about science -- do you love to work with your hands? do you love learning new things and teaching them to other people? do you love using really expensive equipment? do you love the freedom of being your own boss? Only after you know what it is that you want can you formulate your plan to make it happen.