IMO the things that best fit your description would be.
- The iomega zip drive was released in 1994 with a capacity of 100MB, the disks were slightly bigger than a 3.5 inch floppy, but the internal drives still fitted in a standard 3.5 inch bay. The capacity was increased to 250MB in 1998 and 750MB in 2002.
- The imation LS-120 was released in 1997 and it's successor the LS-240 was released in 2001, the numbers representing the size in megabytes of the disk Unlike with the zip drive, ls-120 disks were the same physical size as 3.5 inch floppies and the drives were backwards comaptible with floppy disks.
There were other super-floppy formats too, but afaict these were the two most successful.
However, my experience is that, despite developing new iterations of their formats, by 2000 both of these products were being pushed out by the falling price of CD burners. CD burners had the massive advantage that while you needed a special drive to burn them, you could read them in virtually any PC. They did have some downsides though, mainly that software support for "packet writing" was a mess.
And as you say, in the mid 2000s, USB sticks became a thing. They were first introduced around 2001, but it took some time for them to become common and even longer for their capacities to catch up with CDs/DVDs.
There were also removable media formats based on hard drive technology, these offered larger capacity but were substantially more expensive and the disks were larger. The best known of these probably being the Jazz drive from IOMEGA.