If we're being boring and limiting butterflies:
Rudolf marries Maria Antonietta of Tuscany (maybe his dad's less of a douche about it)
Stef can marry Maria Teresa (or one of her sisters) of Bragança (personally I think a granddaughter of Maria II, like a princess of Saxony might work better).
Franzl will be least important so might get a lesser princess from somewhere (possibly even one who has to convert).
As to the people left without brides:
Stephanie of Belgium to Alfonso XII of Spain
Archduke Karl Ludwig to a Savoyard princess maybe (the Austro-Italian marriage agreement fell flat due to Archduchess Mathilde of Teschen's secret smoking habit; so if that still happens, I could see Austria and Italy wanting to fix bridges. I'd suggest Margherita of Savoy-Genoa, but her married to Carol I of Romania (who she rebuffed OTL) might be fun to see). If no Savoyards are around, then I'm not sure. Hell, he might not need to remarry since he's got two sons already.
Archduke Otto (if Stef pilfers his half-Portuguese Saxon wife) might have different prospects what with the imperial succession looking more secure.
Maria Mercedes de Borbon y Orléans - she was sickly IIRC so she might die before a decent groom is found if Alfonso goes with Stephanie (when he was scouting for an Austrian wife OTL, he privately told one of his friends that he would've preferred to marry Maria Christine's MOTHER to the daughter (gotta love those Spanish royals and their incest

)
Maria Christine of Teschen - either marries to Franzl (like I said, his marriage will be dynastic but not necessarily more than a minor blip on the int'l scene), or becomes a nun as she wanted to.