For me it is Tough Call between Windows 98 SE and Windows ME.
Pros of Windows ME vs 98 se:
Faster boot up time (literally a few seconds on my computer!)
System Restore
Good USB support (I know this can be added to Windows 98 se)
I like the auto completeing functions in Windows Explorer that is on ME.
I think the TCP/IP stack is more stable.
I like the menu affects
the bad:
No restart to dos.
The Unofficial Service pack seems screwed up on Windows ME... The latest doesn't even install the main updates!
It seems the unofficial support of Windows 98 SE is overall better vs Windows ME.