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I went down the H2 road too... even with some help from tools like H2Reg at www.helpware.net, I wasn't impressed with the state of things.
Sure, it worked -- but doing the merge was a pain (both as a developer and as an end user... it took about 60 sec on my 2.4 GHz P4). And doing it properly, in the face of uninstalls/repairs/reinstalls, is a tall order.
Several of our test machines had their whole MSDN indexes blown away, in some non-reproducible test scenarios.
So I'm hot convinced H2 is ready for prime time.
Now, having said that, check out this VS PowerToy...
http://www.gotdotnet.com/team/ide/helpfiles/CustomHelpBuilder.aspx
-S
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