I currently use both types of filters. Personally, I use a cannister for any tank 29 gal and over. I think they're overkill for smaller tanks.
Cannister
Pros: Whisper quiet, powerful, very efficient, very versatile (multiple media baskets), uses inexpensive media, require less maintenance, can be placed under tank out of view
Cons: Expensive, more complex to set up, less convenient to maintain
HOB
Pros: cheap, easy setup, easy maintenance
Cons: Can be noisy, generally less versatile (except for AquaClear HOBs), filter cartridges can be pricey, require more frequent maintenance