OK...I'm not a professional but I'll help you the best I can and use laymen's terms...because I know (being a layman myself) that things can get confusing. I'm sure someone else on the site will expand on what I write. FIRST, yes all of the those exist...and SOOOOO many more. Personally, I don't trust Netmeeting, I've had a VERY bad security instance with that one. But it does have cool functions for business people.
SECOND, the reason you are getting the update invite at start up is one of your friends has invited you, and the version that actually came on your PC is most likely not supported any longer. So you if you want to use MSN you have to go to the newest version. (You could go to a version that's still supported, too confusing so I won't get into that)
THIRD, Windows messenger is, I'm not really sure what the heck it is, except trying to be the other messengers that already exist, and not doing that great of a job at it I might add. (I think it's just basically a messenger without bells and whistles)
FOURTH, I've used Yahoo! for about 7 or 8 years if not 9, so I really like it. And I know they even have a business version that is safer, but I believe you have to pay for that.
I hope this helped a tiny bit. I'm sure someone else may be able to give you more specifics for what you want. Good Luck...and don't get too confused...there are A LOT of messengers out there and it gets confusing. The best thing to do is to stick with one you like...and there's always Trillian, which is interoperable with a bunch of messengers. There's a section for it here on the site, under "others." People really like it, I personally have not used it.
Good Luck all the same!!
(I hope I haven't confused you even more!)