I've done quite a bit of vinyl-to-Cd transfer and find one of the best cleanup apps to be CoolEdit Pro.
Version 2.0 can be a bit troublesome in XP, but the 2.1 upgrade fixes this (and improves the program quite a bit, too.)
For capturing from the disc, I use CD-Wav (a small shareware from Holland -- had it for years) - it's dead easy to use and runs on anything (I have an older machine in the back room that's more-or-less dedicated to file capture of various kinds -- has a tape deck, radio tuner and turntable permanently connected and a removable HD so that captured files can be readily transferred to the main unit for editing.)
I'll describe the basics of my method, which seems to work rather well.
Best way with vinyl is to use Cd-Wav to capture an entire side -- don't attempt to split it.
When capturing, make sure your recording volume isn't overly high -- doesn't matter if its relatively low (CoolEdit can easily fix this), but too high will introduce distortion and getting THAT out is hell's delight!.
Then load the whole track into CoolEdit -- if it's an average vinyl side you should be quite able to see the gaps beween tracks, and you'll also see quite a bit of garbage that you'll want to get rid of (turntable rumble, tape hiss, scratches and other glitches -- a short listen to the first number is usually enough to give you an idea of what's what.)
Don't attempt to do any editing of this track, just select the first song (place cursor at the bginning and shift-click in the space between the first two songs.)
Cut (Ctl-X) the selection, open a second iteration of CoolEdit (Ctl-N) and paste (Ctl-V) the song into it.
Now you can get down to business. Almost all your work from here on will be from the 'Effects' menu -- you can ignore most of the fancy bits.
First, normalise the song (Effects - Amplify - Normalise) -- I generally use a value of 98% for music.
Next, take out all the easily removed defects such as turntable rumble, tape hiss and what-have-you (some computer-soundcard combinations will introduce a whine, you take this out here as well).
Select a period of silence -- as long as possible -- from the inter-song gap -- easiest way is to select a short bit at either end of the song, enlarge it and select silence from this (you don't want to pick up ANY of the song itself.)
Now open Effects - Noise Reduction - Noise Reduction.
In the dialog box, select 'Get Profile From Selection' - OK.
Now exit the dialog, deselect the period of silence and return the display to the full track.
Now re-enter the Noise Reduction dialog and click OK.
When this finishes, I usually run Normalise again.
Now listen to your song -- often that will be all you need do, but frequently there will be unacceptable clicks and pops that need further treatment.
Here you'll use Noise Reduction again, but this time select the first option (Click and Pop Remover).
Here you have several options -- you can get a profile from the entire track and run it, which often works very well (experiment here) and for really stubborn noises you can select the actual point and choose 'Remove Single Click Now', which in version 2.1 is pure magic!.
When satisfied, save your file in the normal way and select 'close'.
You'll be returned to the first instance of CoolEdit, where you can repeat the above on the next song -- working through until the disc side is finished.
This way you don't have to worry about splitting a disc side at all -- it's automatic and you don't need HD space for intermediate files.
There's lots more CoolEdit can do, of course, but this should get most users up and running.
Sound Forge and others work in a similar manner, but my experience has mostly been with CoolEdit, which I've used on-and-off for several years.
Hope this helps some of you.