Generally, STFM and STE's are inter-compatible.
For those you don't know, the ST line is split into two main parts (ignoring the earlier STF's, or STM's, whichever it was) - the STFM and the STE. Both are based on the m68000 (same as the Macintosh line I think).
The STFM I think was the most popular sort of Atari. It was quite basic, and came with TOS 1.02 (the operating system). The STE was an enhanced version, with a blitter chip (for graphics), some stereo features, and a newer TOS 1.62. STFMs and STEs were generally extremely compatible with each other. Few programs required an STE to run, but when they did, it was worth it!
Both machines were often upgraded to TOS 2.06... ahh, those were the days....
Then you get the 1040STFM, 1040STE, 4160STE etc... the numbers only refer to the memory. 520 was 512kb, 1040 was 1MB, 2080 was 2MB etc. The only difference between a 1040 ST and a 520 ST is the amount of RAM.
ST emulators usually emulate an STE, seeing as an STE is essentially an STFM with extra things bolted on. In fact, the different between STFM and STE is so slight, most people refer to them both as the 'Atari ST'. Anything you have which ran on an Atari STFM/E should run on any modern ST emulator.
From the STE Atari then made the 68040-based Falcon 040... and some other machines. But I've never used any of them
That's probably confused a load of people, but I just had to get the nostalgia out of the way
-- Dave