It does appear that the inclusion of "open and not free" packages in
GNOME is an exception, not rule.
If a program is not free, it cannot be in GNOME. Its inclusion would
be a serious mistake.
Has there been such a mistake? The cases you cite don't show any.
On my system out of 109 packages 4 combine GPL/LGPL with BSD license,
one combines GPL/LGPL with MIT (compiz-gnome).
There are two different BSD licenses. Both of them are free software
licenses (see http://www.gnu.org/licenses/license-list.html).
I hope these programs uses the revised BSD license, because that is
compatible with the GPL. The original BSD license is incompatible
with the GNU GPL, so combining the two would violate one license
or the other.
If "MIT" means the X11 license, that is also a free software license.
So it looks like all the software you're talking about is free.
Many people think that only programs under GNU licenses can qualify as
free, but that's not so. For the definition of free software, see
http://www.gnu.org/philosophy/free-sw.html.
There are some licenses which are open source but not free software.
Fortunately they are not used very often. You can find them, more or
less, by comparing the OSI's list of approved licenses with
http://www.gnu.org/licenses/license-list.html. I recall that
Reciprocal Public License one of them; I found a few others but I
don't recall which ones.
I say "more or less" because if a license is not mentioned in
license-list.html, it could be that it is free and we have not yet
studied it. Also, there are many simple licenses that are minor
variations of the BSD licenses or the X11 license; they are free, but
it would be tedious to list them all.
I know of one other way a program can be open source and not free. A
product can come with binaries made from free software source code,
and not let the user change the binaries. Then the source is free
software but that binary is not. The definition of open source is not
concerned with this issue. Thus, the tivoized binary (plus its source
code) would be a program that is open source but not free software. I
mention this issue for completeness' sake, but I don't think it
affects the list of GNOME apps: all these apps can be built and run
from source code.
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