I have no real preference, I just look at the advantages of each solution when I need to choose:
Advantages of cut negatives:
- easier to scan in a home scanner, for lower-quality scans (such as a flatbed scanner with transparency unit): film holders are usually no bigger than 3 or 6*6 frames.
- takes very little space to store
- flat storage (no possible deformation of film due to film being rolled on itself)
Advantages of uncut negatives:
- preserves the full order of the shots. Usually not useful, except if time is really important or if you used some bracketing technique and you absolutely need to know which picture was taken before which other one.
- my local photo retailer charges less for scanning / printing a full film from uncut negative (price per film instead of price per frame), it may be the same for yours
- film is usually stored in a small cardboard or plastic box, which reduces the pressure on the film, and *maybe* allows for better conservation (pieces of film not sticking together). However, the film in this case is not stored flat, and *maybe* this can cause some subtle distortion if the outside extends when the inside does not (this statement being more a "what if" assumption than something I have seen). Being stored as a roll, the film has a tendency to keep that shape when taken out of its box, which makes it more difficult to hold it flat for scanning at home.