The most common reason flash drives get corrupted is impatience. I often refuse to wait to eject flash drives, and I know I'm not the only one. (In my defense, I also tend to make sure nothing critical is only on a flash drive, and you should, too.)
Drives get corrupted when you don't safely remove them because of something called "write cacheing." Essentially, write caching is a feature that improves write speeds. Rather than writing each request as it is received and forcing you to wait, your OS will cache these requests, and fulfill all of them in one fell swoop. When you tell your computer to safely remove or unmount your flash drive, you essentially warn the OS that you're going to remove it, so it writes all requests in its cache to the disk, and tells all background programs to stop accessing it. If you don't wait, you could have items waiting to be written to disk, which could result in a corrupt filesystem.
As for format, I personally prefer ext4 for my flash drives. For Windows, I would say go with NTFS, as ext4 tends to cause problems in Windows. NTFS supports large files, and journals, so it will work pretty well. Filesystem is largely a personal choice, and typically anything that is less prone to corruption is also going to be significantly slower. ZFS is becoming popular, though I don't know whether that works on Windows, and I don't know whether it can be put on a flash drive.
In terms of brands, I don't find a large difference in quality from one to the other. Some have better protection for the connectors, some certainly feel less 'flimsy' (although, surprisingly, I've found that the flimsy ones break less often). I usually just use whatever is cheap.
You should recognize that nothing important should ever be kept solely on flash memory. USB sticks are too easy to lose, step on, or drop into the toilet, etc. Important data should be backed up and kept on at least two distinct drives, and preferably in at least 2 separate physical locations (think fire risk, flood risk, etc).
1We don't do product recomendations on Superuser so specific manufactors won't be listed. Have you determined if the data corrutption came from wear on the device itself or because of it being abused ( i.e. being removed without being ejected first )? I only suggest NTFS, data corruption can be handled a great number of ways, data duplication with verification is only one way. – Ramhound – 2013-05-13T13:07:48.803
@Ramhound I don't know if that would be better, since NTFS doesn't inherently protect against data corruption. FAT32 might be better for flash memory, since there's no journal (and thus less sectors are written to over the life of the drive; I believe this is why most manufacturers suggest FAT32). Might be best to stick with your second suggestion, and either duplicate & verify, or checksum & generate some recovery archives. – Breakthrough – 2013-05-13T13:50:09.573
@Breakthrough - The use of FAT32 would limit the filesize of a given file. Without understanding the cause of the data coruption in a case like this, its tough to say, it wouldn't happen in the future with the FAT32 filesystem. – Ramhound – 2013-05-13T14:03:24.817
@Ramhound agreed there, the 4GB limit is a huge pain. I certainly have used NTFS on some of my own USB drives, but I think it's still worth noting that doing so will probably decrease the lifespan of the drive (depending on the average size of file you write to the drive over its' life). – Breakthrough – 2013-05-13T14:07:56.120
The devices were from at least 2 manufacturers (no brand) and could always be reformatted and used again. Before restoring, it was always possible to extract the majority of the data, although some of the filestructure got lost and some files were corrupted. It is highly likely that they were ejected properly. – Peter – 2013-05-13T14:25:50.353
@Peter - Based on what you describe now it sounds like you run into simple lifetime writes performance issues. Important to purchase a device advertised as high performance. – Ramhound – 2013-05-13T14:30:56.093
I've always assumed the fat32 default selection was made primarily as a lowest common denominator that could be assumed to be supported universally and because it had a lesser patent/etc burden than NTFS. – Dan is Fiddling by Firelight – 2013-05-13T14:50:22.530
@DanNeely in particular, I saw this KB article on Patriot's website: Will my flash drive lose performance if I format it it to NTFS?, which states that
– Breakthrough – 2013-05-13T14:59:20.357Yes, FAT the default file format, is the best suited file type in terms of performance for our USB Flash drives.