I started writing this post as a question, but found the answer by the time I was done, so I thought I'd make it informative.
TortoiseSVN (and probably most other SCC software) will allow you to override the default diff-viewer per file extension or MIME-type, so I was looking for a way to do this is TestStand sequences. I found this snippet in the TestStand help file:
So I plugged in a custom viewer for .seq using the path "C:\Program Files\National Instruments\TestStand 4.2\Bin\SequenceFileDiffer.exe" %base %mine. You'll notice this is a little different than prescribed by the help file - first' date=' the executable name is different and second, there are no quotes around the parameters. For whatever reason, putting quotes around the params broke the paths. Even without quotes, though, it works with fairly long paths (135+ characters) which has spaces in it.
Another plus, IMO, is the diff that pops up isn't the whole sequence editor - just the pane that shows the diff results.
P.S. If you didn't know, TSVN ships with support for diff'ing a whole bunch of MSOffice formats - really handy for comparing documentation revisions!
For the truly lazy, here's a registry file to add the diff for you. Take note, I'm using TestStand 4.2! You'll have to rename it to .reg to merge it.
TortoiseSVN Diff - seq.txt