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If ATW shows 3000 links, it's a safe bet that they're not all going to the home page. This is perfectly okay, but it might mean that your assumptions about how PR is flowing within your own site aren't quite accurate.
Aside from internal link tweaking, the only way to raise PR is to have more outside links coming in to your system. You want every link you've got, and more more more!
Remember that an inbound link that is well worded can have other advantages besides PR.
Its an interesting question because I've heard the proposition that lower PR sites linking to you can actually DECREASE your overall PR value, then if you had numerous of these sites linking to you it could actually weigh down your PR rather than build it... Orrr will these additional sites (or votes) actually act to increase your overall PR? I never really understood this part of the google algo and have heard differnt theories.
I don't think there's much real evidence for anything other than incremental weighting.
Of course, once you're a PR 5, the effect of each PR 2 and 3 site linking to you on your overall PR is going to be virtually insignificant.
[webmasterworld.com...]
I agree we should have a PR faq, I'm getting tired of posting the above link.
Incoming links can't hurt you. Outbound links may or may not hurt or help, nobody is quite sure, but it is suspected that the quality of your outbound links affects the SERPs but not PR. It is part of the other 99 parts of the algo, which we know less about than PR.
PR is pretty well understood. Go ahead and add the links from the high PR sites, do not try to remove the others, they won't hurt you.
A good link from a high PR site is worth way more than a large number of bad links from low PR sites. But all of them help you to some extent.