Applications "sucked out" by Limewire?
 

Was downloading a program (slowly by dial up ISP) so I left Limewire "running". Problem was that it has taken days to restore applications that seem to have been "sucked out" during this process. Found copies on the HD, but running them was as if I was rebooting from new. Lost Mail (Address Book & Mailboxes plus contents), iTunes, Safari Bookmarks, Library, and Desktop just to name a few. What happened? I am loathe to try downloading or "sharing" again.
endee013

That sounds very odd!!! Yes Java for OSX is less than efficient & if LW runs for a long time can use up lots of Virtual Memory (HDD space.)

Some suggestions to minimise this effect:

Go to LW's prefs>Speed & tick disable Ultrapeer Cap. & press apply button.
Set both uplds & downlds to autoclear.
Close all LW windows you don't need open at that time. (I only keep the main search & downld window open.)
If you're not in front of your comp, then hide LW in the dock.
Close old search results by control-clicking the search result tab & choosing close search (they can go stagnant after a while anyway since people are continually going on & offline.)
Reduce uplds to about 70-80% or more.
Whilst LW is open, click on top of the Progress bar so all incomplete files are organised by % downlded. Then select 1st at 0% & scroll down to last & select it whilst holding down SHIFT key also all at 0% are selected, then press the Stop button. Then go to your incomplete folder & view it in list mode & click on size column so all are arranged by size. Now delete all those at 0 KB. This will speed up opening of LW & reduce stress on connections. Another description is here: Tip: Purge the Downloads Queue!
You might also consider reducing shared files if you have multiple thousands of them. Good luck.

Also Don't use the Resume button on all incomplete files. This can have side-fx such as affect LW's connection quality. May queue your files for much much longer. This will also stress LW & your comp. If you use Resume/Find sources then just apply it to a couple or so at one time. Particularly on dial up.

Make sure you have plenty of HDD space available & also RAM.

I'd recommend you do a system repair using Disk Utility on your installation disk (find it in the utilities folder.) Might be worth seeing these also: 1. OSX Troubleshooting Links--Please add, 2. Resolving Disk, Permission, and Cache Corruption