Top journals don't necessarily contain the best papers
For many fields, especially in the natural sciences, the "top-tier" are not just looking for well-done, well-written research reports. Instead, they have an explicit editorial goal of finding papers that are impactful and interesting to a wide, interdisciplinary audience. For example, Nature wants manuscripts that
- are of outstanding scientific importance, and
- reach a conclusion of interest to an interdisciplinary readership.
- technique reported will have significant impacts on communities of fellow researchers
- the therapeutic effect reported will provide significant impact on an important disease.
In practice, this means that they often select for 'hot' or controversial topics, the use of exciting new techniques, and surprising, counterintuitive results. As a result, the zeitgeist of the field is probably the major determinant of whether your paper gets accepted in a 'glamorous' journal like Science, Nature, or PNAS. Quality is obviously important too: even the trendiest paper won't get in if the experiments are obviously flawed or the writing is impenetrable (usually!). However, it is manifestly not true that the best quality papers are published in the best quality journals, or conversely, that everything published in a well-regarded journal is gold.
To add some specific examples, Physical Reviws rejected Theodore Maiman's description of the laser, Physics Letters didn't want the Higgs model, and Nature declined the first reports on MRI, the Krebs Cycle, and(!) the cell cycle. Paul Lauterbur, whose MRI paper was rejected from Nature--but nevertheless won him a Nobel Prize (2003)--has quipped that "You could write the entire history of science in the last 50 years in terms of papers rejected by Science or Nature."
On the hand, these journals are also full of papers that seemed exciting at the time, but either went nowhere or turned out to be fatally flawed (e.g., arsenic-based DNA, water memory, and so on).
How do you decide where to publish?
If you already have a target venue in mind, you can often submit a presubmission enquiry. Each journal handles them slightly differently, but they almost always contain the manuscript title and abstract, and often include a short discussion of the results and why the journal's audience may care about them. The editor will reply, often in a few days, to tell you if the proposed article is a good fit for the journal. While you often don't get much feedback at this stage, it can help you avoid journal-specific scutwork, like reformatting the text or redrawing figures. Occasionally, editors will also mention concerns related to a specific topic: Current Biology told us, for example, that while they were interested in the topic generally, they also felt that much of the existing literature was not very good, and so they would be expecting very rigorous controls.
If you don't have a "target journal", you need to think about the potential audience for your paper. There are many journals which specialize in particular techniques (e.g., J Neurophysiology, for neurophysiological experiments), topics (Attention and Perception for studies of, well, attention and perception), and application (J. Neural Engineering). Browsing your own reference list may help: your paper is likely on-topic at the journal you cite most!
Finally, I would quickly browse through a few complete issues of your candidates. For example, while Journal of Vision and Vision Research are both nominally interested in anything pertaining to seeing, Journal of Vision skews very strongly towards human behavioral experiments. Although you could submit other kinds of work there--and people occasionally do--there are probably better venues for experiments with other techniques or animal subjects.