These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Les Yay: Plenty as the series goes on, most noticeably between Vanessa and Madlax. Limelda's obsession with Madlax also borders on Foe Yay.
Tear Jerker: Many, notably the fate of poor Ann Moray, who dies in the only episode in which she appears, after being mind-controlled into killing her father. The fact that it's heavily implied that Margaret was in love with her does not help. Nor does the music.
Pretty much every character death qualifies, but a special mention has to go to Elenore who has probably the biggest Wham Line in the series when she explains why she's so devoted to Margaret and dies shortly afterwards.
Elenore: Because Miss Margaret, you are my........family.