Personally I'm pretty fond of modifying the input record seperator:

local $/="</end>\n";
my @group = map {[/<ref id="([^"]+)">/g]} <DATA>;

print "New Group: @$_\n" for @group;

__END__
<ref id="ref1">
<ref id="ref2">
<ref id="ref3">
</end>
<ref id="ref4">
<ref id="ref5">
</end>
<ref id="ref6">
<ref id="ref7">
<ref id="ref8">
</end>
[download]

Outputs:
New Group: ref1 ref2 ref3
New Group: ref4 ref5
New Group: ref6 ref7 ref8

(edit: Ah, so is GrandFather, read right past his response, 'ooops')