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Someone correct me if I'm wrong but I believe most compact flash storage cards are CF I and compact flash device cards are CF II. Basically, I think any CF card fits.
As for SD cards, MiniSD is half the size of a regular SD and MicroSD is even smaller. However, both Mini and MicroSD should be backwards compatible with the standard SD interface, providing that you place them in an SD-adapter. Practically all MiniSDs I've found in stores come with an SD card adapter already. Basically, you place the Mini/MicroSD into the SD adapter (which is the size of a regular SD card) and place the adapter into your SD slot so yes, they amount to the same thing.
The reason why I brought up the topic of Mini/MicroSD is because 90% of Pocket PC phones these days only support either Mini or MicroSD. So, if you wanted your cards to carry on over to these devices, Mini/MicroSD will be the way to go. However, if your plan is to stay with your current iPAQ for some time, a regular SD card is good enough.
As for which to buy, that's purely your preference. You mentioned wanting to leave the CF open for addon cards, so go with an SD/MiniSD/MicroSD option. As mentioned before, any of these three types of SD cards should work, providing that you have an SD adapter if you choose Mini/MicroSD.
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