A couple case studies of photographers presenting their photos in different ways. I am not a big fan of auto-play slideshows or repetitive loading indicators. Have a look and make up your own mind. 

Elizabeth Weinberg  Philip Toledano  Todd Hido Noah Kalina  Reed Young  David Maisel  Hedi Slimane  Ben Huff  Grant Cornett  Jessica Hilltout  Timothy Hogan John Wright  Rankin Igor Askarov  Djordje Zlatanovic

Over the past years I have tried out many many different ways of presenting (and backing-up) my photographs online. MobileMe Gallery, Viewbook (above album is done with Viewbook), BananAlbum, JAlbumPhotoshelter, Flickr embedding, Gallery, Picasa, simple HTML presentation, home-brew Flash auto-size-adjusting album, plain horizontal photo-strip, Apple Aperture photo website generator, Dreamweaver click-thumbnail-to-enlarge album, fancy film-strip-perforation portfolio, 6million Wordpress gallery plug-ins and so on and so on.
And what is the result of all this time racking search? Confusion! There is no ultimate way of presenting (backing-up) photographs online. All tools listed above have their pros & cons. Let me list some of them quickly.

MobileMe Gallery
Pros - Nice photo overview page with resizable thumbnails. Very convenient when using Aperture for synchronising. Doesn't use Flash, so albums work nicely on the iPhone/touch/pad etc. 
Cons - Can't embed album into website. No customisation beyond standard features. Not easy to integrate own domain name. No viewing statistics aka Google Analytics. Can't un-brand. 

Pros - Good web-based image manager. Well thought out features for customising albums. Integrated website maker. Good full-screen mode. Pro account allows for un-branding. Flash based, which means that Google doesn't soak up all your images. Flash is good and bad at the same time. Easy for people to embed your albums. Password protection. Use own domain name.
Cons - Non really - wait. 10MB file size upload limit. No Aperture plugin currently. 

Flickr slideshow embedding (not Flickr website presentation)
Pros - Good & fast full-screen mode. Great image manager. Syncs now with Aperture 3. 
Cons - Flickr branded. Slideshow opening screen displays a not so nice looking big play button and flickr buddy icon. 20MB files size upload limit. 

Pros - Upload and retain any file format and file size. Good e-commerce tools. Lots of customisation features. Image presentation, sales and back-up at the same time. 
Cons - Minor ones. I can't remember any major deal-breaker. 

Confusion Conclusion: Viewbook for clean uncluttered professional image presentation, embedding, JPG sharing, Photoshelter for selling images and back-up, Flickr for cheap image storage and sharing, MobileMe with Gallery for some more image storage, presentation and sharing madness.
One precondition for me using any photo manager/presenter is the ability to change photos, caption, order, size etc in a quick & easy way. If I can't do this I won't use it. I prefer using paid cloud/web services aka SaaS (Software as a Service) tools like Viewbook, Photoshelter, Flickr or MobileMe over desktop software like JAlbum, BanaAlbum or Dreamweaver + Flash. Good luck with finding your preferred tool. Trial them and get it over and done.