How to judge quality of manuscript to decide whether to submit to high-ranked journal? I am not talking about whether I can submit a paper on subject A to a journal on subject B. 

My question is: 

How do I know how good my paper is? I could of course just send it to the best journal in the field, and see what they say, but I also don't want to embarrass myself and waste their time. If, however, it is very good and would be accepted by such a journal, it would be unwise to publish this in a lower ranked journal I would think.
As a couple of others have noted, generally speaking you will get a feel for this as you read the literature in your field. However, your target journal may have published criteria for publication. For example, PLoS Pathogens states:

To be considered for publication in PLOS Pathogens, any given
manuscript must satisfy the following criteria:

Originality
High importance to researchers in the field
High importance and broad interest to the community of researchers    studying pathogens and pathogen-host interactions
Rigorous methodology
Substantial evidence for its conclusions


For most journals now, the reviewer is asked to score your paper against areas like this as well as provide general comments.
For comparison PLoS ONE states simply:


The study presents the results of primary scientific research.
Results reported have not been published elsewhere.
Experiments, statistics, and other analyses are performed to a high technical standard and are described in sufficient detail.
Conclusions are presented in an appropriate fashion and are supported by the data.
The article is presented in an intelligible fashion and is written in standard English.
The research meets all applicable standards for the ethics of experimentation and research integrity.
The article adheres to appropriate reporting guidelines and community standards for data availability.


Basically, as long as it isn't fundamentally flawed it stands a good chance with PLoS ONE.
The biggest differences between journals are typically how important your findings are, and to how many people. From personal experience the 'broad interest' criterion (where you are asked as a reviewer to comment on it) is the one I most often find myself scoring papers badly on; most people don't think about this enough.
Without wishing to sound negative: as the others have said, if you genuinely can't tell whether your own paper is 'good' then it probably isn't going to set the world on fire. Then again, nothing ventured, nothing gained; you won't generally get 'blacklisted' for submitting a low-quality manuscript to a journal, and it doesn't cost anything. So if you're being modest but are secretly quite proud of it, you might as well give it a chance with a high-impact journal first. You can always resubmit somewhere else if it gets rejected.
One final word of advice, since it sounds like you're fairly new to this: don't get upset, embarrassed or disheartened if your submission is rejected or torn to shreds by a reviewer. Rejection is common (especially if you're ambitious about the journals you submit to), harsh and apparently unfair reviewer comments even more so, and the editor will normally take the reviewers' side unless they're clearly in the wrong. (And if you stick with academia, you'll find this last bit this goes double for grant applications!)