- GNU WGET
- Backing up a Wordpress site: "wget --no-parent --no-clobber --html-extension --recursive --convert-links --page-requisites --user=<username> --password=<password> <path>"
- Wget with WARC output
- HTTrack - HTTrack options
- Heritrix -- what archive.org use
- Pavuk -- a bit flaky, but very flexible
- Beautiful Soup - Python library for web scraping
- Scrapy - Fast python library for web scraping
- Splinter - Web app acceptance testing library for Python -- could be used along with a scraping lib to extract data from hard-to-reach places
- WiLiSe WikiLink Search - Python script to get links to specific pages of a site through the search in a Wiki (MediaWiki-type) has the api.php accessible or extension LinkSearch enabled (the project is still very immature and at the moment the code is only available in this SVN repository).
Pinboard is a convenient social bookmarking service that will archive copies of all your bookmarks for online viewing. The catch is that it costs $9.25 just to join, plus $25/year for the archival feature and you can only download archives of your 25 most recent bookmarks in a particular category. This may pose problems if you ever need to get your data out in a hurry.