You can have Linkbot recheck just selected directories, or redo the whole site after you've made corrections. You can even schedule it to check the site on a regular basis. Linkbot uses the CSE HTML Validator, and a flexible tool it is. You can configure it just about any way imaginable, and it will check your HTML for compliance with whatever standards you desire. I found Linkbot to be a well-designed and powerful program.
Documentation is ample, and most commands are easy to figure out.
It has the features and flexibility to be suitable for use on large commercial sites. I tested it on The Web Developer's Journal, which has 1260 pages, connecting through a cable modem. Checking the whole site took a while, but overall the program seemed stable and robust. Wisebot Wisebot was a rather unique tool that scans your site, and automatically creates a set of navigation tools for it. WiseBot has been discontinued, and is no longer available.