As with everything digital, garbage in = garbage out.
That being said, the nicer equipment you use from the cartridge to and including the soundcard, the better your cd will sound.
After several years, many upgrades and dinking around, I have a pretty nice system for doing this.
A Pioneer PL-55DX equipped with an Audio Technica AT70 cartridge (their best spherical cartridge...and for some reason, sphericals seem to run a little 'quieter' on questionable records) is fed to a NAD Integrated Amp, which serves as the phono preamp. That in turn is fed to the breakout box of a GINA by Echo sound card (It has a physical external box for inputs, outputs) and is recorded in Sonic Foundry SoundForge 6.
I try to keep processing to a minimum. I use the default "Remove Clicks and Crackles" setting called "Default for Vinyl Records" from SF's noise reduction package.
I record each side as a single track, and then run the noise reduction. Then I break each track out by cutting and pasting it into a new track, and completely remove all information up to the very first note on each track manually. On the tail end of each track, if it's a fade ending, I fade the tail part of the fade and then mute the track up to the start of the very next track. If it ends cold, I'll do a gentle fade on the sibilance or room ring, and do the same...mute information after that up til the next track start. This insures that there's absolute silence between tracks, and the NR gets most, if not all, of the clicks during the song. The result is about as good as it gets.
As always, there's room for improvement, but if you get a decent phono pre-amp, a decent turntable and cartridge, and a very nice sound card (this is the hardest part, most of them are junk), and the software of your choice for cleanup (and under-processing is preferred to over-processing), you'll do well also.
