Fics relating specifically to Will/Lyra are(although I recommend reading them all):
1) like gold to ayery thinnesse beate (Will/Lyra) by lalaietha
A door missed - or left apurpose - can be found even when you aren't looking for it.
2) that kind of grateful (Will/Lyra) by lalaietha
Follows 'like gold to aeyry thinnesse beate'; the morning after.
3)you are safe here you know (Will/Lyra) by lalaietha
Will visits his mother on Christmas Eve.
4) through a glass, darkly (Will/Lyra) by Callie
Will Parry finds an object that grants him a long-held wish.