Currently, you have to manually search the histories of the files in the change set you are trying to accept. Having the system both tell you what the gaps are, and give you automated ways to either fill or merge out the gaps is a high priority work item that unfortunately did not make it into 4.0. See work items 128329 and 24822.

Cheers,
Geoff

How can I tell which change sets are missing while accepting?

From IBM documentation- Resolving gaps in change history:

Because those dependencies have not been met, there is a gap in the change history for the component that can only be resolved by finding the missing change sets and accepting them in the correct order, or by accepting a change as a Rational Team Concert source control patch.

In RTC 4.0.5 we delivered additional support when trying to accept change sets which have a gap (often encountered when trying to backport fixes). In a very brief summary of the feature, when you accept change sets with a gap, you can now follow a gap workflow that accepts one change set at a time and, for change sets that contain gaps, creates a new change set (with aided traceability), that contains the equivalent changes. This means users will not have to accept the change sets 'as a patch'. Applying change sets as a patch has limitations compared to the new workflow (as discussed in the article below).
This feature is summarized in the RTC 4.0.5 'New & Noteworthy' page:  https://jazz.net/downloads/rational-team-concert/releases/4.0.5?p=news#scm-improve-usability-405-m1
Below are some videos which show this feature:
-Accepting multiple change sets with gaps in the RTC 4.0.5 client for Eclipse IDE: https://www.youtube.com/watch?v=28raag5RdzU
-Accepting a change set with a gap in the RTC 4.0.5 client for Eclipse IDE: https://www.youtube.com/watch?v=TucVu_BgB7E

In RTC 5.0 we added a "fill the gap" feature where the change sets that fill the gap are shown to the user, allowing them to either accept all the change sets or to continue with the gap workflow that was available in RTC 4.0.5.
This feature is summarized in the RTC 5.0 'New & Noteworthy' page: https://jazz.net/downloads/rational-team-concert/releases/5.0?p=news#eclipse-fill-gaps

The classes that are involved for filling the gap include (available in RTC 5.0):
client side: IWorkspaceConnection.findChangeSetsToAcceptToFillGap(...)
server side: IScmQueryService.findChangeSetsToAcceptToFillGap(...)

Both features are explained in detail in the "Improved Gap Handling for SCM" article: https://jazz.net/library/article/1372