Flash has its advantages for photographers, in that "right-clicking" of images, or dragging them to the desktop, is not available, but with the constant movement in flash plug-ins (visitors needing updates), and the delayed loading, I'm not a fan of the functionality struggles for some visitors. I'm a "KISS" guy (Keep It Simple Stu...") when it comes to web applications/sites and prefer that IF flash is used, it's used very sparingly. As a visitor, nothing gets me to leave a site quicker than to have to sit and wait for a flash library to load. If a page chugs to load the library I usually just close the window. Visit a high-end company's site selling products or service via $250K website and see how madding it is to wait for this huge flash movie to load when you enter the site. It's just silly IMO. Not everyone has a fast connection to the internet. I'm currently sitting in Bangkok and while my connection is pretty fast (faster than my home in the U.S.) most here have much, much slower connection speeds. It can be torture waiting for some sites to load.
Of course, I just visited one flash-based site which loaded fast, was clean looking, and functioned well, so done right Flash can be nice. However, I just stripped a Flash-driven client section from my site because I hated the image quality. There are some issues with colors and details b/n flash and simple HTML pages and it has been a point of frustration for some fussy folks who have both flash and non-flash offerings (to accommodate visitors without the needed plug-ins). Colors often differ in the two different settings. In my case, I was simply using SimpleViewer to generate the slide show and incorporated into my site for clients to flip through the images. I hated the images, but the clients could not tell the difference, my sister-in-law could not see it (a disinterested party), and another observer wasn't moved by the difference. To me the difference is obvious and drastic (in this example), so I pulled it and rebuilt the section using the same method I do for my other stuff. SlideshowPro is another tool that can be used, so I may try that next time. I'm not a Flash developer, so I have to just sort of limp along and cobble, though I am comfortable with (X)HTML and CSS coding at modest levels.
I find that for "client viewing" or just plain old convenience to visitors, a page of thumbnails is very nice. This can be sectioned by category or client, or whatever. If one offers 100 proofs to someone, they can flip through the full-size images and "ooh and ahh", but it's difficult to cull without a full view of thumbs. This is quite easy to do. If commenting is allowed on the images, the client can mark them with a number rating, or ask you to hide certain images from view (i.e. rejections), etc. One could also incorporate a rating tool separately as well (like a five star thingy) via JavaScript.
I don't recall the details of Jono's site, and may not know which one you refer too, but I have visited one that he used for sharing his M9 experiences with all of us (that was great of him) and I didn't see anything there that was complicated coding. I'll have to revisit to see if I can offer a more useful comment. I don't recall if he has a different site for his other photography.
And I probably should have lead with this: do you want to make something yourself, find a turnkey package, higher a team of developers and designers...?
Some folks like to use SmugMug or Zenfolio, but I like to tinker on my own.