Over the past 6 months, I have seen an increasing number of leading online web apps displaying in-app messages.
Maybe this is because we provide an in-app messaging solution so I am more attuned to it, but I think, rather, that we are seeing a growing trend.
Here are the top use cases that I have seen:

1. Educate about a new feature

As Google made its move from Google Apps to Google Drive, some of the user experience changed.  This callout educates users on the difference.

And Google also teaches users about new features in Google Docs.

Hootsuite does the same to highlight their new Auto-Schedule feature
These messages work well because they are tied to new features that no one using the application has seen.  It would be annoying to get such a message if I had already used the feature.   Consider targeting your in-app messages based on feature usage to address this scenario.

2. Making a new user’s experience better

Salesforce  used this callout to encourage me to communicate with a co-worker who had not yet used Chatter.

3. Encouragement to upsell

 Desk.com notifies me of the number of days left in my trial and encourages me to upgrade now.  In addition, problems are highlighted for me.

4.  Reminder to do a regular activity

Here, Hubspot is just simply reminding me to actually set up my social media integration.  How cool would it be if they could occasionally and appropriately remind me of the need to engage in social media when my discipline/habit there is slipping
This is what Google is doing here.  Giving me a reminder to get back on Google AdWords and pour in my money after I stopped for a few days.

Problems Overcome

One of the problems with in-app messaging is that historically it's been tied to the dev team.  This has limited marketing’s ability to be flexible, try out campaigns.
The other problem has been the lack of data on a per-user and per-account basis to easily behaviorally target users to only show messages appropriate to them.
We’ve built our solution to address both these problems.  Try it out.