Well lesse now*warning,spoilers ahead*
In Clamp,they hint many MANY different couples.Some of my favorite are X/1999'S KamuiXFuuma,and Cardcaptor Sakura's TooyaXYuuki.
In Fruits Basket Tooru and Kyou seen to be kept in hiding,until much later in the series where the couple is beyond obvious(hell,they even get Yuuki a new girl)
In Kaine,Kaine and Die *cannot*be more than friends>_<
In Utena *gasps from breath*UtenaXAnthy,MikiXJuri,MikiXhis sister,JuriXShiori,NanamiXTouga,MikageXthat young boy(brainfart)Man...that anime needs to set its prioritys straight>_<
In Pet Shop Of Horrors,Count DXLeon seems MORE than obvious!
In Battle Royale(all versions)If Mitsu didn't have sucha psycological issue,one could assume her and Yuchiro would have been inevitable.
In Fushigi Yuugi,SoiXNakago seemed iffy,but...
and in Marmalade Boy and INuyasha,KeiXSuezu and SessoumaruXKagura seemed hinted.