Think I just upgraded from 2.8.6 to 2.9.8 in an unconventional fashion, but it gets past the "old version cannot be removed" error that everyone seems to be hating recently.
downloaded the "Windows with no built-in JVM" .zip file you can find by clicking the "here" in "....try here" at the bottom of the basic download page. The files extract into a 2.9.8 folder wherever you decide to put it. I backed up the old 2.8.6 folder first(just in case it didn't work) and then cut and pasted all the files inside 2.9.8 into the 2.8.6 folder. There was no new .exe file in the dowload archive, so doing this uses the existing old .exe file(Hmmm, maybe that's the way it's been working for sometime...) Anyway, clicking on my old LimeWire shortcut launced it in the usual way, with only the "Upgrade to Pro" nag and had the correct version in "About" and the newest Limewire as well complete with the new cutsie icons on the view tabs and everything. It's seems to be workin normally, don't know if it's 100% right, but it's connnecting, and downloading, and that's good enough for me. If it decides to start flubbing up, I'll just slap the old 2.8.6 guts right back in there, until LimeWire 3.whatever.whatever is released, hopefully with a properly functioning installer. Anyone else who wants to give all that a try, go for it. just hold on to your working version somewhere. Oh, I read some of the posts about deleting registry entries( I didn't even go there, that thing still scares me) and all that other weed pulling...and the only thing I tried was uninstalling using add/remove programs. I saw a progress bar for like a second, and that was it. Nothing else happened, and nothing was uninstalled or changed in anyway. That always ticks me off a little bit. Even a Third party program claiming to remove "stubborn programs" had exactly the same effect. (Ultra WinCleaner One Click!...actually) so I mean...WTF!?!? I enjoy limewire and for now have plans to keep it, but just how DO you get it all out, when you want it out. Including out of the add/remove programs list?
Good Luck People,
Scat Man

I had the same problem
(running win98se).

This is what I did to fix it.

1. Delete limewire folder
2. Run regedit, ctrl+f (find)
3. search for "limewire" (without quotation marks)
4. Delete all reg keys and reg dir's associated with limewire (I.E. find, delete, "f3" {find again...}, delete, until it is no more)
5. Install v2.98
6. Run limewire

Note: I get v2.98 to run, but now it takes a few minutes to execute, previous versions never did that.

Your results may vary.