I have searched through the posts and did not see an answer for this.  Is there a program that will let me set up a position, analyze it (as a clarification I mean me and not the computer) with all the variations that I see, and save it.  So I can reference it as my games progress.

there are two programmes that will do what you want. They are both free

babaschess  http://www.babaschess.net/download.asp

and arena sorry dont have the url to hand for that. but google will find it for you.

which to use is a matter of personal choice so try them both.

hope this helps PG 

Thanks for the freeware suggestions, anyone have comercial program suggestions? or other freeware programs?

Commercially Fritz is one of the best

Arena for game analysis + online gaming

More:
www.playwitharena.com

Engines:
http://www.playwitharena.com/directory/engines.htm

Commercial Fritz or Chessbase

Fritz 11 and Chessbase 9 would be an ideal set up to have. You can set up positions using both and fritz 11 will analyse for you.

One more question regarding all of the great suggestions, does ant one run these programs on Vista?

seuss68 wrote: One more question regarding all of the great suggestions, does ant one run these programs on Vista?

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 I do. No problems to report.

Thanks Graw81 for the information.

I have decided to give babaschess a try.  So far it looks to be what I was looking for.  Thanks again for all of the information.