We have released a beta version of our software, and as we talked to people who started using it, we have found that a lot of the features (which we thought were essential) were not known and not used by the users.
What are the possible ways to inform the application users about the features of the application? I personally find the “Tip of the day” popups extremely annoying and disable them quickly. Are there better ways?
It depends on the: features, application, platform and users.
There is no magic usability dial that you can just turn or button you can just push.
Even within the above there may be multiple ways that a feature can be made more discoverable but it the right one(s?) may be dependent upon how much flexibility you have. In that you’ve just released the app to actual users, I’m guessing that you’re not in a position to restructure the app or make dramatic changes to the way it is architected to improve discoverablity.
This is why usablity testing (with real users) should be started early (in the development process) and done often.
If you can provide a more specific example of a feature that you want to make more discoverable then you may get a more sepcific answer. And if you ask it at https://ux.stackexchange.com/ you may get a better answer still.