SIDedit.exe    : sid header editor + disassembler, made in perl2exe,
                 unmaintained. I personally don't use it but others find it handy.
siddiag.exe    : diagnostic of header/code errors, memory usage map, trims
                 unused memory at end of sid file                         
sidclean.exe   : newer cleaner also trims at start if needed. still in beta but
                 will replace siddiag and siplay2/hacked                       
sidknown.exe   : identifies duplicates by actually playing the sid and
                 generating md5 hashes from the sid usage             
sidusage.exe   : detailed usage checker, generates a map read by siderror
siderror.exe   : reads maps generated by sidusage and reports badreads/bad
                 execution etc                                            
sldetect.exe   : songleghts.txt generator, actually plays the sids to detect
                 when they loop or stop emitting sounds to determine the    
                 lenghts                                                
sldb_merge.exe : accessory to sldetect.exe, to merge partial outputs
                 eliminating dupes (so sldetect could be run on updates instead
                 of the whole hvsc)                                            
siddump.exe    : hacked to also dump the executed disassembly code mostly used
                 to compare song output of similar/equal songs but also to spot
                 execution errors                                              

<?xml version="1.0" encoding="UTF-8"?>
<SID type="RSID">
	<Header>
		<LoadAddress="0000">
		<InitAddress="4000">
		<PlayAddress="0000">
		<Songs="20">
		<StartSong="1">
		<Name="Arkanoid">
		<Author="Martin Galway">
		<Released="1987 Imagine">
		<RelocStart="0000">
		<RelocPages="00">
		<Flags>
			<!--   	0 = built-in music player,
					1 = Compute!'s Sidplayer MUS data, music player must be merged.	-->
			<Format="0">
			<!-- 	0 = C64 compatible,
					1 = PlaySID specific (PSID v2NG)
					2 = C64 BASIC flag (RSID) -->
			<Player="0">
			<!-- 	0 = Unknown,
					1 = PAL,
					2 = NTSC,
					3 = PAL and NTSC. -->
			<Clock="1">
			<!--	0 = Unknown,
					1 = MOS6581,
					2 = MOS8580,
					3 = MOS6581 and MOS8580 -->
			<SidModel="1">
		</Flags>
	</Header>
	<STIL>
		<Author>
			<Comment="Martin Galway's own comments are denoted (MG).
				'I will never do rearrangements of those tunes on other instruments,
				the SID is what they're meant to be heard on. It would not be
				'updating' them to put them onto a different instrument. If you ever
				hear music from me on today's instruments, the tunes will be all-new
				(and probably a lot better).' (MG)">
			</Comment>
		</Author>	
		<SID>
			<Comment="This is the very first published tune on the C64 that used samples.
				'I'm glad you spotted 'Cobra' on the Spectrum, whose tune I was in
				love with and HAD to use somewhere else...! I figured no-one would
				complain if I used it a year later on the C64.' (MG) (It got used in
				Arkanoid.)
				'Q: How did you get involved with using sampled sounds?
				MG: I figured out how samples were played by hacking into someone
				else's code... OK, I admit it... It was a drum synthesizer package
				called Digidrums, actually, so you could still say I was the first to
				include samples in a piece of music. [...] Never would I claim to have
				invented that technique, I just got it published first. In fact, I
				couldn't really figure out where they got the sample data, just that
				they were wiggling the volume register, so I tried to make up my own
				drum sample sounds in realtime - which is the flatulence stuff that
				shipped in 'Arkanoid'. [...] After the project was in the shops I
				gained access to some real drum samples, and I slid those into my own
				custom version of the tune. The one that's in the shops is kind of a
				collage of farts & burps, don't you think? [...] Later I was able to
				acquire some proper drum samples and by 'Game Over' it got quite
				sophisticated.' (MG)">
			</Comment>
		</SID>	
	</STIL>
	<Songs>
		<Song1>
			<Length="2:22">
			<STIL>
				<Title="Cobra (Title) [from the Spectrum game]">
				<Artist="Martin Galway">
				<Comment="'I'm glad you spotted 'Cobra' on the Spectrum, whose tune I was in
					love with and HAD to use somewhere else...! I figured no-one would
					complain if I used it a year later [for Arkanoid] on the C64.' (MG)">
			</STIL>
		</Song1>
		<Song2>
			<Length="1:17">
			<STIL>
				<Title="Hiscore [from the arcade game Arkanoid - Revenge of Doh]">
				<Artist="Hisayoshi Ogura (OGR/Zuntata)">
			</STIL>
		</Song2>
	</Songs>
	<Binary>
		(Binary code goes here)
	</Binary>
</SID>

"XSID", $????????
"IN", $0026 // Info (always $60 bytes in PSID)
"A", $04, "Drax" // Author
"N", $0a ,"Test Music" // Name
"C", $15, "198x Maniacs of Noise" // Copyright
"FL", $????  // Flags
...
"DA", $???? // Data
...

"XSID", $????????
"IN", $0026 // Info (always $60 bytes in PSID)
"A", $04, "Drax" // Author
"N", $0a ,"Test Music" // Name
"C", $15, "198x Maniacs of Noise" // Copyright
"FL", $????  // Flags
...
"DA", $???? // Data
...

"A",$04,"Drax" // Author

"ADDR",$02,$d420 // Address of 2nd sid

The whole core of the MD5 code is very small:

        // Include C64 data.
        myMD5.append(cache.get()+fileOffset,info.c64dataLen);
        unsigned char tmp[2];

        // Include INIT and PLAY address.
        writeLEword(tmp,info.initAddr);
        myMD5.append(tmp,sizeof(tmp));
        writeLEword(tmp,info.playAddr);
        myMD5.append(tmp,sizeof(tmp));
        // Include number of songs.
        writeLEword(tmp,info.songs);
        myMD5.append(tmp,sizeof(tmp));
        // Include song speed for each song.
        for (unsigned int s = 1; s <= info.songs; s++)
        {
            selectSong(s);
            myMD5.append(&info.songSpeed,sizeof(info.songSpeed));
        }
        // Deal with PSID v2NG clock speed flags: Let only NTSC
        // clock speed change the MD5 fingerprint. That way the
        // fingerprint of a PAL-speed sidtune in PSID v1, v2, and
        // PSID v2NG format is the same.
        if ( info.clockSpeed == SIDTUNE_CLOCK_NTSC )
            myMD5.append(&info.clockSpeed,sizeof(info.clockSpeed));

        // NB! If the fingerprint is used as an index into a
        // song-lengths database or cache, modify above code to
        // allow for PSID v2NG files which have clock speed set to
        // SIDTUNE_CLOCK_ANY. If the SID player program fully
        // supports the SIDTUNE_CLOCK_ANY setting, a sidtune could
        // either create two different fingerprints depending on
        // the clock speed chosen by the player, or there could be
        // two different values stored in the database/cache.

But the "selectSong(s)" is the not trivial part of the whole calculation which sets the songSpeed for every song.

If you convert the selectSong method in the loop, for the things needed for the MD5 calculation, you will get:

   uint8 u8CiaSpeed = 60;
   uint8 u8VblSpeed = 0;

   for (i = 0; I < u16NumSongs; i++) {
      if (!boPSIDSpecific) {
        if (i < 31)  // check tune 0-30 (bit 0 - 30)
          boVbiSpeed = !(u32Speed & (1 << i));
        else
          boVbiSpeed = !(u32Speed & (1 << 31));// last bit sets speed for tunes >31
      } else {
        // old PlaySID implementation
        boVbiSpeed = !(u32Speed & (1 << (i % 32)));
      }

      // speed setting
      if (boVbiSpeed)
        md5_append(&u8VblSpeed, 1);
      else
        md5_append(&u8CiaSpeed, 1);
   }

    m = hashlib.md5()
    m.update(sid_data)
    m.update(struct.pack("<H", sid_header[HDR_INITADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_PLAYADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_SONGS]))
    for i in range(sid_header[HDR_SONGS]):
        if sid_header[HDR_SPEED] & (1<<i):
            m.update(chr(60))
        else:
            m.update(chr(0))

    m = hashlib.md5()
    m.update(sid_data[2:])
    m.update(struct.pack("<H", sid_header[HDR_INITADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_PLAYADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_SONGS]))
    for i in range(sid_header[HDR_SONGS]):
        if sid_header[HDR_SPEED] & (1<<i):
            m.update(chr(60))
        else:
            m.update(chr(0))

    sid_header = unpack_header(data)
    sid_version = sid_header[HDR_VERSION]
    sid_data = data[sid_header[HDR_DATAOFFSET]:]
    m = hashlib.md5()
    m.update(sid_data[2:])
    m.update(struct.pack("<H", sid_header[HDR_INITADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_PLAYADDRESS]))
    m.update(struct.pack("<H", sid_header[HDR_SONGS]))
    for i in range(sid_header[HDR_SONGS]):
        if sid_header[HDR_MAGIC] == "RSID":
            m.update(chr(60))
        else:
            if sid_header[HDR_SPEED] & (1<<min(i, 31)):
                m.update(chr(60))
            else:
                m.update(chr(0))
    if sid_version == 2:
        if (sid_header[HDR_FLAGS] & 0x0c) == 0x08:
            m.update(chr(2))

/MUSICIANS/J/JCH/Tecnetium.sid
{'COMM': 'I always get mixed feelings when I play this
  music. The title- tune is\nlong and I put a lot of work
  into it in april 1989, but today I can\nhear loads of
  harmonic errors here and there. The game was done for
  a\nsideways shoot\'em up which a couple of totally
  unknown danish guys was\nmaking. They soon lost all
  interest in their game, however. The\nhiscore theme was a
  conversion of the old Cliff Richard
  hit\n"Congratulations" done right out my head. I always
  wanted to make such\na hiscore tune, because I always
  thought Rob Hubbard did it all wrong\nwhen he made "sad"
  hiscore tunes. It is a sad thing when the game\nends, but
  getting a high score is supposed to be a GOOD thing! :)',
 'TUNS': [{'LENG': 23330816, 'NAME': 'Title Screen'},
          {'ARTI': 'Cliff Richard',
           'LENG': 5963776,
           'TITL': 'Congratulations'},
          {'LENG': 262144},
          {'LENG': 196608},
          {'LENG': 2883584},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 196608, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 196608, 'LOOP': 'G'},
          {'LENG': 131072, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'},
          {'LENG': 65536, 'LOOP': 'G'}]}