I just use Nero Wave Editor. Of course this means manually seperating the files by individual tracks after recording a whole LP side, but it's worth it to me to preserve irreplaceable recordings.
It also has nice features for filtering, editing volume and so forth considering that it's just something I got as an oem software. In the case of bad scratches and stuff, I've also become good at manually editing those out. It takes some time, but I find it rewarding to do a good job restoring a damaged track.