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It is horses for courses really. I bet everyone has a different window size. I'd say it depends on what you are displaying. TOC/Index/Search/Glossary tabs, browse sequences, topic content (e.g. images), etc. etc. would all have a bearing on the best size for the window. My advice? Pick a "standard" and go with it.
We always try to avoid overwhelming the user and make the help window relative to the application window. This is one advantage of using CSH to call up the topic window and the initial call to hide the TOC/Index and Search. If the help window hides the application, the user may find it hard to refer between the two.
As you rightly say, the user should always have the ability to change the size of the window if they desire.
You may also like to consider the average computer screen size used by your users. Some companies issue everyone with 19in screens or higher, others are not so generous.
I know this is not much help as it does not give you a direct help window size, but there is a lot to consider if you need to come up with a standard. Don't forget to also specify standard for images that will be included in the help system. You may want to consider a maximum width for screen shots for example as these may be hidden if they do not comfortable fit in the help topic window.
It is also something to discuss with the developers.
Just as a guide, I'm currently working on a project that displays the help window at 600*500. This does not hide the application window and gives the user the ability to toggle between the application and help. It is good to give the user a bit of control.
Hope this helps and good luck