I'm still a big fan of 5mm LEDs, especially in arrays. At this point in time the better ones are more efficient than power LEDs. They're easily scalable to outputs in the low hundreds of lumens. They don't require heatsinking although they do require laying out a PC board with good thermal paths. IMHO their color rendering is better than power LEDs like Luxeons, especially in the deeper reds. The beam artifacts mostly cancel in larger arrays. They don't require the added complexity of optics. While tints do vary in large arrays these also tend to cancel.
Sure, they do have their downsides. For starters the lifespan of the whites is only a fraction of silicon encapsulated power white LEDs. For many uses however the lifespan will exceed the useful life of the device they're in. Next the driving requirements may be more complex, and the PCB layout certainly is. At this point in time the total costs for a given amount of lumens using 5mm LEDs may well exceed a similar project using power LEDs. On the one hand you have more expensive heatsinking required for power LEDs but on the other you have the insertion costs of many pieces of 5mm LEDs for a given lumen output (cheap labor can largely negate this factor). Taken as a whole though if you want a certain amount of lumens while maximizing your run time 5mm is probably the best way to go.
There are certainly ways to improve 5mm LEDs further. Lifetime should match their larger cousins. Indeed, Seoul Semiconductor has already fixed this problem. Cost per lumen should be on par or less. Basically, given the $2.50 or so per piece price for 100 lumen power LEDs this means that 5 lumen 5mm LEDs must be priced under $0.10 once insertion costs are taken into account. A better thermal path is needed as well, perhaps via a heavier lead frame.
Although they have their fans here, I'd say the 5 watt quad-die LEDs are the least attractive choice. They fail badly on cost per lumen. They're harder to focus. Their output is only marginally more than the better binned 3 watters at this point. The lifetime of the whites is abysmal.