Mr. Nutz 2 - Hoppin' Mad for the Megadrive could be an easy one it's just a matter of getting the total lenghs of all the tracks from the direct ripped from the AMIGA TFMX tracks:
http://www.exotica.org.uk/wiki/Mr._Nutz_-_Hoppin%27_MadWarning: These TFMX files are multitracks and must have the Deliplayer instelled to get the lenghs until the BZR playlists are fixed on that type of TFMX and to skip a subtrack use the + & - buttons as some are impossible to be quick enough on the draw do do via button on like there is a death music before the Opening theme on one of the files.
Then all thats need to do is the logging the tracks of the Megadrive version in the options menu then cheating to win or playing through it properly to get the ending screen music or hacking it in but all the other musics seem to be playable in the menu natively and comparing those times to the MD version.
Stone Protectors is another one of those with the same type of options but that you can use any player you like on it to get the lenghs as it has a native rip for the SNES and also has music in it's options menu.
Edit: You don't even need a player to listen to the lenghs on this game as the tracklist and lenghs are logged on the SNES Music site already so dnt' need to get them yourself:
Track: Title: Length:
01 Kemco 00:02
02 Introduction 02:21
03 Main Theme 03:25
04 Player Select 00:20
05 Opening 00:21
06 Snowy Village 01:10
07 Snowy Village (Tension) 00:24
08 First Encounter with Zink 00:40
09 Story Progress 00:58
10 Crystal Mine 01:05
11 Crystal Mine (Tension) 00:16
12 Second Encounter with Zink 00:48
13 Further Story Progress 00:24
14 Downward 01:39
15 Downward (Tension) 00:14
16 Dance with the Launa Boss 00:30
17 Success 00:32
18 Beach Party 00:59
19 Beach Party (Tension) 00:10
20 Beachball with Tackle Jackal 00:38
21 It's Getting Dramatic, Babe 00:39
22 Forest of Mythrandir 01:50
23 Forest of Mythrandir (Tension) 00:12
24 Wraith 00:40
25 Story of Danger 00:20
26 Bizarre Bazaar 01:17
27 Bizarre Bazaar (Tension) 00:08
28 Frank Does It! 00:49
29 We Need a Volunteer 00:52
30 Approaching the Castle 01:17
31 Approaching the Castle (Tension) 00:19
32 Zink at Last 00:31
33 Zink is an Idiot 00:24
34 In the Castle 02:05
35 In the Castle (Tension) 00:14
36 Sucker Puncher 00:28
37 Sucker Puncher Sucks 00:21
38 Final Showdown 00:21
39 The Laboratory 02:25
40 The Laboratory (Tension) 00:16
41 Predatron 00:35
42 Everyone Has Failed Me 00:34
43 Throne Hall 01:38
44 Throne Hall (Tension) 00:11
45 Lord Zok 00:30
46 Victory Celebration (part 1) 03:00
47 Victory Celebration (part 2) 00:41
48 Staff Roll 01:18
49 Game Over 00:06
50 Tournament Battle 04:08
51 Snowy Village (Megamix) 01:11
52 Crystal Mine (Megamix) 01:08
53 Downward (Megamix) 01:02
54 Beach Party (Megamix) 01:07
55 Forest of Mythrandir (Megamix) 01:21
56 Bizarre Bazaar (Megamix) 01:07
57 Approaching the Castle (Megamix) 00:49
58 In the Castle (Megamix) 01:01
59 The Laboratory (Megamix) 00:51
60 Throne Hall (Megamix) 01:21
b01 Unknown Jingle 00:05
s01 Character Selection 00:02
s02 Go 00:03
s03 1-up 00:02
s04 Stage Completed 00:02
Hope that helps for tracklists to get some Stone Protectors and Mr. Nutz 2 rips. But then again some times could be off due to framerate differences between consoles but these are approx lenghs to help get our SEGA rips proper lengh.