Some things take really long to transfer, while other things don't take long at all, regardless of the file size. Some of the things that take extra long are Egoboo and the Java Run Time folders. I'm guessing this is because they ARE sligtly larger than some files, but not THAT much larger than other things I've put on here that take much less time. Is it because they're composed of more individual files or what?

I believe so

I can confirm that, I've noticed it before too.
I just tried on my microSD:

256x 512kb files = 128MB took 1min 30secs to transfer
1x 128MB file = 128MB took 31 seconds to transfer.

I remember when I transfered 3gigs of pictures, it took like forever, but if they were zipped in one file it would take few minutes
When there is invidual files its hard to build them all again.

Writing one file -> Dir Read/Write -> FAT Read(s) -> File Write -> FAT Write(s)

So if you write 256 512kb files, it means a lot of Dir read/write, FAT read/write, rather than just one dir read/write and a FAT read/write every 128 clusters.

With an intelligent caching file system, you could reduce the time considerably, but neither Linux or Windows support such a feature, and instead simply cache all reads/writes. In fact, Windows is worse, as it disables write caching for removable drives.

You can enable write caching in Windows, which makes it quicker, but you also have to eject the drive manually. I've found that transferring loads of stuff (entire music collection) takes much less time with write caching (i.e. under Linux) than it does without.

Not only that, if a game is composed of hundreds of very small files it takes 10+ minutes to load and then uses twice the space of it's actual size because of clusters not being properly filled.

That only happened to me on one game, I don't recall the game, and it was just an isolated incident of bad design.

I know SuperTux has loads and loads of small files. Instead of having one big tilemap, each tile is an individual file, which is very bad design indeed.

Word. Almost like Phobia III

What about OS X?

No, it has about the same support as Linux does.

Yep, as the basic Windows users are too stupid to unmount a card (not talking about anybody here) and would destroy their filesystems every few seconds

I'm too stupid, trashed my 2gb sandisk about a month ago. Tried reformating it on a few different devices and with different readers, but none have worked. Sometimes it just says the format cannot be completed, others it says it's done it, but afterwards the card is just the same.

Anyone have any ideas let me know, but i've probably already tried.

You can try the SDFormatter from Panasonic, which can do a low-level-format and create new lowlevel partitions on the SD-Card.
Another (even better working) way is DD from an identical card (either use Linux, which has DD included, or a windows compiled version. Does work with that, I already did that a few times).

If all that does fail, your SD Card is TECHNICALLY defective, good time to return it to the dealer.