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With attached test.zip and svn revision 67006,
$ ./python.exe test.zip 
> /Users/sasha/Work/python-svn/trunk/test.zip/__main__.py(2)f()
(Pdb) l
[EOF]
With pdb.patch:
$ ./python.exe test.zip 
> /Users/sasha/Work/python-svn/trunk/test.zip/__main__.py(2)f()
-> pass
(Pdb) l
 1 	def f():
 2 ->	 pass
 3 	
 4 	import pdb
 5 	pdb.runcall(f)
 6 	
 7 	 
[EOF]

Just to confirm - this is specific to __main__.py right?
The problem is actually with runpy not being able to set __file__
correctly, rather than being pdb specific.

No, I only used __main__.py to make it easy to reproduce the problem.
Pdb will not be able to access code in any module with a custom
__loader__. For example, if you move f() to foo.py inside test.zip
and import it from __main__, you will see the same issue. My patch
gives linecache.getlines() called by Pdb access to module's globs and
thus to its __loader__ . It has nothing to do with runpy.
> The problem is actually with runpy not being able to set __file__
> correctly, rather than being pdb specific.
You must be thinking issue4197 where two distinct problems are
adressed: first, the crash due to __file__ set to None by runpy and
second, missing globs parameter to linecache.getlines() in doctest
module.
My patch, doctest-1.patch works around the first issue and fixes the second.

Off-topic: How to report a bug tracker bug?
The e-mail I sent in response to Nick's post started with:
"""
On Wed, Dec 3, 2008 at 3:51 PM, Nick Coghlan <report@bugs.python.org> 
wrote:
> Just to confirm - this is specific to __main__.py right?
>
No, I only used __main__.py to make it easy to reproduce the problem.
...
"""
But the first two lines got eaten by the tracker. Should I open an 
issue here and if so, what do I set as a component?

Issues with the tracker itself go in the meta tracker (see the "Report
Tracker Problem" link at the bottom of the left hand navigation menu).
It's a separate tracker in order to handle cases where the main tracker
is actually down in addition to problems with the functionality.
And you're right that the get_filename() limitation is only part of the
story rather than all of it (for both this and other issues). I'll still
try to look at them all in one go this weekend though.

The patch hasn't been accepted for the trunk, yet, so it is out of scope
for 2.5.3. Retargetting.

Fixed for 2.7 in r67750.
Will be ported to 2.6, 3.0 and 3.1.

Final revisions for fix:
2.7 = r67751 (there was a new test file missing from the initial checkin)
2.6 = r67752
3.1 = r67753
3.0 = r67754