Thank you for suggesting the ABX tests. They were very illuminating. After 10 tests, I was able to tell a difference 100% between FCEUMM and Nestopia 1.44 in RA 0.9.8.2. However, when testing against Nestopia 1.44 Undead in Windows, I could not perceive a difference between the two recordings after Replaygain adjustment. There may have been a slight frequency difference, but I did not feel confident that I could ABX them, and that may have been due to my recording methods anyway. In my opinion, it sounds like the RA port of Nestopia Undead faithfully reproduces the sound of the Windows port. I call this a non-issue for the RetroArch team.
Otherwise, I performed the Genesis tests first, and was easily able to tell a difference 100% between the standalone version and the RA port using Sonic & Knuckles. However, after the NES tests, I feel I need to revisit them and do a bit more testing before making an official report. I need to get to work now, so it will have to wait until tonight. If anyone wants to use my samples to provide ABX results as well, please do. WAVs of all samples are included, and also the replaygain'ed lossless FLAC files I used for the NES testing.
Here are copies of my ABX results. Please remember that the NES results just prove that there is a difference between FCEUMM and Nestopia 1.44 Undead, but I believe this has nothing to do with RA. The non-normalized NES WAV results are not included to reduce post size, but are included in the uploaded zip.
https://anonfiles.com/file/581ebc95e1381d383295f9b8c4d00594
foo_abx 1.3.4 report
foobar2000 v1.1.6
2013/02/07 08:25:09
File A: FCEUMM - Contra.flac
File B: RA Nestopia 1.44 - Contra.flac
08:25:09 : Test started.
08:25:37 : 01/01 50.0%
08:25:44 : 02/02 25.0%
08:25:48 : 03/03 12.5%
08:25:53 : 04/04 6.3%
08:25:59 : 05/05 3.1%
08:26:07 : 06/06 1.6%
08:26:12 : 07/07 0.8%
08:26:17 : 08/08 0.4%
08:26:21 : 09/09 0.2%
08:26:33 : 10/10 0.1%
08:26:35 : Test finished.
----------
Total: 10/10 (0.1%)
foo_abx 1.3.4 report
foobar2000 v1.1.6
2013/02/07 08:04:29
File A: Genesis Plus GX 1.7.3.wav
File B: RA .9.8.2 Genesis Plus GX 1.7.3.wav
08:04:29 : Test started.
08:04:36 : 01/01 50.0%
08:04:45 : 02/02 25.0%
08:04:53 : 03/03 12.5%
08:05:00 : 04/04 6.3%
08:05:08 : 05/05 3.1%
08:05:15 : 06/06 1.6%
08:05:22 : 07/07 0.8%
08:05:29 : 08/08 0.4%
08:05:35 : 09/09 0.2%
08:05:41 : 10/10 0.1%
08:07:19 : Test finished.
----------
Total: 10/10 (0.1%)