Most scanners come complete with reasonable, own marque, stand alone software. Normally this is fairly basic but for average scanning purposes it is adequate.
The better quality scanners come complete with their own marque software plus a more professional, third party programme that allows you to control almost every aspect of scanning.
Quite often, the higher quality scanners also include image editing programmes like Adobe Photoshop Elements that allow you to manipulate your scanned (and other) images to correct colour balance, contrast and exposure etc. Sometimes software to enable you to create panoramic views and build web pages is also included with the software bundle.
If you want to have total control over nearly every aspect of you images then look for scanners that include specialist scanning and editing software like that made by Silverfast for example.
This type of software lets you remove blemishes or remove and replace image elements as you wish. You also get the options of using "home", "auto" and full professional modes- the latter giving you a huge range of scanning options.
Several of these scanners come complete with a full set of frames that allow you to insert your negatives or slides so that they are correctly aligned in the scanner. They also cover the range from 35mm and all the intermediate format sizes up to 5 in x 4 in. The 35mm frames permit you to scan a full 36 negative frames in one go. Each image can then be individually adjusted.
Special frames are also included to allow you to scan mounted slides in several formats. You simply load the negatives or slides into the appropriate frame and select the correct option (negatives, slides, colour, black and white etc.)