Free tool like Snagit which can capture scrolling Window?

The free version of FastStone Capture will capture a scrolling web page. Works best with IE but also works with FF (it scrolls the window very slowly) and kinda works with Chrome (page is OK but it messes up the the scroll bars).

There's also PicPick (use the 'Capture Window Control' command) which works with IE and Firefox though won't scroll in Chrome.

I use the free ScreenGrab add-on for Firefox, which can capture a selection of a page, the visible portion, or the whole page past the scroll area. In addition, it can also copy to clipboard, or save as JPG or PNG. I've been using it for over a year now with no ill effects -- it's great.

If you're using Firefox, then FireShot might be what you're looking for.

Web Screen Capture - a free stand-alone web site and web page screenshot and thumbnail utility.