One reason I haven't created linkbacks for my site yet is because I can't decide how to handle the case when I get links from a homepage. Mark Pilgrim makes the linkbacks auto-expire, which I'm not sure I'd want to do. It seems like you lose a record of who linked to you awhile ago - the link still may be valid. Although I'm really not sure what algorithm he uses to expire linkbacks.
In any case, if you get a link from someone's homepage, and if you program in your linkback checker some knowledge of common blogging tools and permalink url formats, I bet you could do a pretty good job of auto-discovering the appropriate permalink. I'd say it would have to work 90-95% of the time to be accurate enough, but I bet you could get that. It's only for weirdos like me who wrote their own system with links like no-one else's that it'd be hard for.
If there was only "a standard" for identifying permalinks...
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