I personally consider LinkAssistant to the best tool for checking back links and for everithing concerning Reciprocal Link Exchange Management. Sometimes it is a bit stupid , but if those guys are going to develop their tool just as they are doing it now - I feel safe for my link partners: LinkAssistant will keep an eye on them
I suppose I'll throw in my two cents because I'm a good guy. For links, Link Capture or Arelis, for PPC, Ad Gooroo, for general all around, Web CEO and Internet Business Promoter.
I also use Xenu LinkSleuth to make sure that all on-site and external-pointing links are OK, as well as WebBug to check that redirects work OK, and are delivered with correct status code.