HT? You mean Hyper-threading?
The main advantage that the Pentium 4 processors have over Athlon 64 processors in single application settings is in encoding. In particular, video encoding.
However, there is one area where Pentium 4 processors shine, and that's multi-application environments. If you've got ten programs running at once, would you want one fast computer or two slower ones? Two slower ones! Bingo. Hyperthreading is a feature of the Pentium 4 that creates a virtual processor, allowing the processor to handle more than one "thread" (application, basically) simultaneously. This has a very good effect on multi-tasking.
However, multi-core processors are on their way, and that'll make Hyperthreading into just another joke.
As for the availability problem with Athlon 64s...It is present, to a degree. That's why Dell is now strongly considering implementing AMD Opteron-using servers into their lineup. They're not, however, considering implementing Athlon 64 processors into their lineup. Why? AMD can't meet the demand for consumer processors. They can meet them on high-end stations, and they can meet them in the locations they're implemented now, but they can't take even half of what Dell would have to shove on them. This has nothing to do with the lack of PCI-Express-using notebooks, however.
That's caused by a pair of things. One is a marketing impetus - Intel seems to be pushing very strongly to have the top-of-the-line notebook of every manufacturer an Intel model. That's why there was no 8750/whatever the number would be for an Athlon 64-based 8790 type system. Another is simply the lack of chipsets. There are barely any PCI-Express motherboards out for Athlon 64 processors, even in the desktop market. We can't expect too much in the mobile market right now.