...I know that with time and usage, our computers collects junk files that make it run slower...
I think that is mostly a myth. A file that is not currently being accessed at the time that you are trying to access another file will have absolutely no bearing on speed, so it really does not matter how many files you have on your HDD, with one exception (see #1):
Generally speaking there are 2 things that can make a computer slower over time, as far as the HDD goes (many more not related to the HDD):
1) file fragmentation. This can only cause a minor slowdown, and it will not really become a factor unless you fill the drive more than 85%. It does not really become problematic until 90 or 95%, but then, exponentially so. It is much worse on Windows than on Mac HFS+.
2) slow consistent failure of the HDD in its ability to read and write. This will happen gradually over time to all HDDs that do not fail for some other, catastrophic reason, such as a failed HBA card, bearings wearing out, a head crash from a blow to the HDD while spinning, etc. The media becomes less reliable over time, and the HDD sometimes tries to read sectors many times in a row to get the data off, which is where the slowdown comes from.
But then migration to a new Mac is the perfect time for spring cleaning and creating a good backup strategy. Here is what I do (and what I did when I migrated from a 2003 PB to a 2011 MBA, which had a smaller 256 SSD HDD).
First I went through the old Mac's HDD and deleted all files that I know for sure that I really don't care about. Then I made a TM backup to an external HDD. Then I went through the old Mac's HDD and moved files that I wanted to save but probably would not need on the MBA, and just saved those in a folder to that HDD. That way I can browse for those files without the hassle of going into TM. Then I put that x drive on the shelf.
Then I connected a second external HDD, and moved another copy of those same files there. Then I went through the old Mac's HDD and deleted all of the files that I was "pretty sure" that I would not need (and remember, those are now backed up) including a lot of "Rosetta" files that would not run under Lion anyway, and made a TM backup of that to the second x HDD, which became my working, incremental backup. Then I restored those files from TM to the new MBA.
This meant I had only relevant files on the MBA, with two backups of those files (actually 2 backups on each x drive), and a single copy of the "junk" files on the first x drive.
Now, since I also had virtually all of those files resident on 2 other older Macs, including those "junk" files, I was covered pretty good. But if you don't have that, it is probably a good idea to then make a duplicate of the first x drive using Carbon Copy Cloner and move that off site, which then gives you full backup to the full backup.
And to be really safe, buy yet another external and alternate TM backups to those two x drives, which means you have 2 backup copies of everything from 2 backups ago, and one backup copy of everything from 1 backup ago.
But that may not really make that much sense for questionable files; 2 or even 1 backup might make more sense. After all, if you have a HDD cluttered by files you really don't need, then you are a candidate for the TV show "Hoarders", and there is a point where spending lots of time making lots of backups of irrelevant files is much the same thing. Just like in real life, you have to eventually jettison stuff you no longer need, and this is the perfect time to stress that sort of self-discipline.
On the other hand, HDDs are cheap, you can make backups easily, and it is a chore/timesuck to pick through all the files on your HDD and toss what does not matter and keep what does; it is much easier to keep everything. Spotlight will still find what you are looking for, although having it search through irrelevant files will indeed slow things down.
The strategy you pick is all dependent on how much storage space you have, how good of a backup plan you want to implement, and how much time you want to invest (personally, I find tossing outdated files liberating). You could also just clone the HDD and reimage the new Mac with that image.
Bottom line, I recommend TM for the migration, although it used to be so much easier with firewire. I had two identical PBs, and when I bought the second one I just hooked it up to the other one using firewire target mode, clicked OK and walked away. Later I came back and I had two nearly virtual clones. The data on both was exactly the same, and the new one had no fragmentation.
