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Originally Posted by whitelyt
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It's not really about FAT32 being better than FAT16 or vice versa. It is really all about how you use your storage card. FAT16 works better for larger, fewer files. So if you use your card for multimedia files for example (video, MP3s) it is better to use FAT16. FAT32 on the other hand works better for many smaller files. So if you use your card strictly for data storage and application files then FAT32 is better.
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whitelyt is dead on... I have 2 storage cards: a 1GB card that is used for storing movies and music (hence I have it formatted FAT16) and a 512MB card that I install games and extra applications on (and, guess what, it's formatted FAT32!) and it makes sure I have close-to-optimal performance depending on what I'm doing. Chances are if I'm listening to music or watching movies, I'm not playing a game or navigating GPS at the same time (that's just me) and vice versa. So I will only use one card or the other at any given time.
PocketMechanic actually gives you the option to choose what you are using the storage card for (multimedia, applications, storing back-ups, maps, etc.) and will format the storage card to the optimal format for you. That is one advantage I found of PocketMechanic over FlashFormat (because beyond what I just wrote in the previous paragraph, I'm dumb about FAT.)
I prefer NTFS anyway.
Actually, if you want to get really geeky, we can talk about WINFS.
I'll stop now. Seriously.