Well, coming from the D1, you need to change your thinking a bit. Unlike the D1, the D3 has a locked bootloader. Thus, the D3 init sequence has to be hijacked, so to speak, to trick the phone into booting into recovery. So, the D3 requires two separate concepts: That of the bootstrap, and that of CWM recovery. In other words, on the D3, you need a software bootstrap installed to get into recovery. Of course you need recovery flashed, too.
So, for the most part, ClockworkMod Recovery (CWM) is CWM. The differences lie in the bootstrap.
The very first bootstrap was Hash's, which has since been abandoned. It didn't allow entry into CWM from a cold-start (power up) reboot, but only from within his bootstrap app on a fully functioning phone. Not good for a soft brick. A great first effort, but it's now merged with Koush's bootstrap. Unfortunately, in the event you installed Hash's original bootstrap, you have to be sure to remove Hash's bootstrap before using Koush's, or you have problems. That old original Hash bootstrap isn't around anymore I don't think, so unless you jumped on the bandwagon the first two days that bootstrapper was invented, you don't have to worry about this issue. Update: wrong! Do NOT install any bootstrap mentioned in any droid-life articles. That's the original Hash bootstrap. Bad!
Now, there is a bit of confusion here, in that the newer Koush's bootstraps have been implemented by Hashcode. Thus, you have to understand that Hash's original bootstrap is different than Hash's implementation of Koush's bootstraps. Clear as mud??
So, at present, there are two Koush bootstraps provided by Hashcode. The first is the Droid 3 bootstrapper, available in the market, which has the same problem as Hash's original bootstrapper, in that it doesn't allow access to CWM from a cold-start power up condition. However, it is compatible with Rom Manager, which the original Hash bootstrapper wasn't. Again, whether you enter CWM from Rom Manager, or from within the bootstrapper app, you obviously need a fully functioning phone. Not good if you've bricked.
Finally you have what Hash calls the "tweaked" Koush bootstrapper (from his website), which allows you access to CWM from either Rom Manager, the bootstrapper app, or if the phone's bricked, from from a cold boot using BP tools (fastboot menu: power up + M on keyboard). It's the best of all possible worlds. It also has some tricks that allow a bootlooping phone to enter CWM automatically via the use of a semaphore that's set and released strategically as the phone is booted and once it functional.
The Safestrap bootstrapper is ONLY for those wanting to boot the CyanogenMod ROM. It uses a different technique, something called a "sandbox" which keeps the original ROM intact. It's kind of like being able to dual boot your phone. Eventually, CyanogenMod will be booted with the same method as the other ROMS.
All that being said, it boils down to really three choices:
1) Use the safestrap bootstrap for booting the CyanogenMod ROM only.
2) Use the D3 bootstrapper in the market for everything else, including ROMs other than CyanogenMod, and for using Rom Manager and making NANDROID backups.
3) Use the tweaked D3 bootstrapper available from Hash's website, which does all described in 2), as well as allowing entry from
a cold boot via fastboot BP tools.
As Hashcode points out, the bootstrapper is stored on /system and can be overwritten when a new ROM is installed. So, whenever changing ROMs, realize that the appropriate bootstrap will likely have to be reinstalled.
Also REMEMBER that this discussion has been all about the bootstrapper. However, the Droid 3 bootstrap app DOES install CWM 5.0.2.6 as well. Or you can install CWM from Rom Manager. However, ROM Manager does not install the bootstrap. You need both to have an effective alternative recovery.
Hope this helps more than it hurt
Neall
Corrections inserted above: 1) Hash points out in his blog that the bootstrap app does install CWM. 2). Do not install any bootstrap mentioned in (or referenced to) the droid-life article on D3 bootstrap. That's the original (outdated) Hash bootstrap.