Personally I mainly use Pubmed, ACM, Web of science, and Google Scholar to find relevant literature. Do I reach 100% recall or am I still in danger of missing important scientific literature? Which indexing services for the literature are you using?
In my experience, 100% recall of relevant literature even for a relatively focused project is not possible. In the 'harvesting' phase of gathering literature during ongoing research, I use the tools you list plus journal TOCs, citeulike's citegeist and increasingly google reader/twitter feeds. During the more 'targeted' phase of writing a paper/grant, I rely on JANE to reveal the papers I have missed. JANE, like eTBLAST, ranks your document versus medline abstracts via term similarity profiles to find relevant papers, journals and authors. Just pop your manuscript into JANE, hit scramble to anonymize your work, and submit to see how many papers have escaped your notice (and hope that you haven't been scooped five years ago :)
Additionally you can use http://highwire.stanford.edu/ for a full-text search, and it returns a direct link to pdf file.
I would recommend to include DBLP / IEEE Xpress to your list. They cover significant amount of computer science oriented bioinformatics abstract and full-length literature and conference proceeding.
You could also use RSS feeds to keep track of journals. In terms of organizing papers, I've liked using mendeley.
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