I know it's obvious, but MIDI music sounds different on different computers. What is mainly responsible for that? Is it mainly the sound card (the most obvious thing), the MIDI playing program, or even the operating system? As I expected (because my last several computers were much older than this one, which I built last year), the MIDIs sound less digital and more like music that wasn't made with a MIDI keyboard. But I didn't expect them to sound so different from what they sounded like on the Windows Media Player running on sound cards from the mid-90s to early 2000s.

A MIDI file is just a series of instructions to a synthesizer, (or another piece of digital equipment, but that's another question) if the synth is different then the sound may be different. MIDI itself is just a glorified serial protocol. You may have a synth like the famous opl2 and 3 series that directly creates the analog sounds you hear or you may have a "wavetable" setup which references small recorded samples for the notes. Wavetables are generally considered by most people to sound better. Newer OSs, generally include some kind of wavetable setup that redirects the samples to your sound card, this takes only a trivial amount of modern processing power. Older sound cards synthesized the sounds directly with oscillators and filters.

Too bad. These sound good, but I like the old MIDI sound better.

You could get the "older" sound a couple of ways if you really wanted to. One way would be to use sampled "synth" sounds in the wavetable, another way would be to use an external synth that works the "old" way. I suggest a really cheap Casio or mid '90s Yamaha. I doubt you have any ISA slots to plug an old SB16 into; the newer ones don't have an OPL chip. I used to have a Linux program that mimicked an analog synth, but I've forgotten the name and it only had direct controls, meaning you couldn't play MIDI files with it.

That's a thought. Some of my MIDI files are so good that I would pay a reasonable amount of money for an old sound card. I don't even know what an ISA slot is.

But is the sound influenced in any way by how the sound card works with Linux? Or should I expect these MIDI files to sound the same if this computer were running Windows?

ISA is what they had before PCI. The newest mobo with an ISA slot I've seen was from around 2003. Now, I'm pretty sure there are still some specialty boards that have ISA slots for legacy hardware decryptors and such, but I wouldn't know where to get one. The easiest way is to look around the 'net for Timidity patch sets that emulate an old synth. I don't know where to find those either, but I'll bet they exist. Lots of people like that old "analog" sound. It reminds me of old NES games. One other thing you could try is installing a SID player and converting your .mid files to .sid and playing them that way. It's kind of crazy but I've seen dumber things work. There's also a project called ADPlug that is supposed to emulate an old ADlib sound card. That might be the sound you're looking for. I got it to work once with XMMS, of all things.

No, Linux doesn't really have anything to do with how MIDIs sound, it's all the sound card and drivers.

Exactly! And several of my MIDIs are indeed NES video game themes. In that category, I've collected the "The Legend of Zelda" original theme; several pieces from the Teenage Mutant Ninja Turtles games (including the underwater theme from the original); at least three from Maniac Mansion; a few racing game themes; and the "Chill" music from Dr. Mario. The Zelda and Maniac Mansion pieces are great, but the others are mediocre.
My other MIDIs are also of varying quality. Some of them, such as the two versions I found of a Bob Seger hit, are as good as or better than the non-MIDI music they are based on; but others (such as the version of Herb Alpert's "Rise") are just weird curiosities.
I should mention that none of them are made by me. I found them all online, some in the late nineties when the Internet still seemed young and new to someone who didn't use it until circa 1994.

Most new cards doesn't have a midi synth. That has cons and pros.

So, most of them use a software synth to play midi, and in that case, it's the software which counts. It's not usually the player which do the conversion (though it's possible, but not a common thing). Most players use the synth installed in your OS, the player doesn't care if it's a software or hardware synth and it doesn't need to know about that either. It just sends notes and instrument numbers, and the synth does the rest of the work.

That synth needs a proper instrument table so it knows what sound is to be played when you say "play C-2 with instrument number 11". Most hardware synths can be programmed with different instrument sets, just like you'd configure a midi piano. Software synths need the same. To change how your synth sounds you just need to load a new soundfont patchset. The question here is "which one can give you the sounds that you like", and there I can't help you.

There are lots of soundfonts in the net, some for free, some are propietary and will require the payment of a given quantity (that can vary depending on the author and the quality of the samples. For example:

http://www.sf2midi.com/

Just google "free midi soundfonts" to get an idea. Once you have a soundfont you can load it in your synth and all the instruments will be reprogrammed with the new soundfont. How this is done depends on the synth you use. So first you will have to find what synth software you are using. Two popular ones for linux are timitidy++ and fluidsynth.

EDITED: Also, I *think* but not sure that dosbox can play midis without having any synth software loaded. You might want to try a DOS midi player under dosbox and see if that works for you. At least, the midi stuff for kyrandia and similar games play ok there, from what I remember.

I went and checked today and ADPlug is definitely in the Ubuntu repos so it might be in the Mepis ones as well, and it has an XMMS plugin. It emulates an OPL2 chip and sounds just like an NES. No hassle at all, too, just install it, activate the plugin, and browse for a .mid file. You might have to de-activate the Timidity plugin, if you have one in XMMS as well.