It really all depends on your application. If all the checkboxes are related, then it wouldn't be a big deal to store them as a comma-separated value in a single field, (so long as you know how to parse the field for later use). A good example would be days of the week stored as "Sun Mon Tue Wed Thu Fri Sat" in a single field. You'd know that if 'Thu' wasn't there, they must not have checked Thursday for some reason. Easy enough...
However, if you have many checkboxes for unrelated information, it might get more time consuming to remember the reason for each value instead of having a descriptive table field. Readability is also an issue. You might be the only developer, so it may be easy for you to remember what "1,0,0,1,1,1,0,0,0,1" means, but for anyone else, they'd have to dig through all the code.
--Brad Fears