Crap. The mencoder profile is failing because the mencoder.conf must have changed at some point. Go into the DTb settings app and edit the "Export to Ipod using Mencoder" profile. Edit the mencoder step and pick "x264/AAC" (I can't remember exactly what it's called, but there's only one) for 1st pass, and "None" for 2nd pass. That should fix it. While you're there, check the "Convert with ffmpeg" action in the profile and make sure it has "Remux to MP4" selected. If it's blank or incorrect, you might need an updated ffmpeg.conf (see the Wiki page for the link)
I still recommend ffmpeg over AVIVO or mencoder. AVIVO is great if you can get your Directshow filters to play nice. If you can't, or if there's file corruption, it will fail randomly. Mencoder is a great idea that needs some work. It eliminates the splicing step by using EDL, but the output needs to be remuxed by ffmpeg before the iPod will like it, so that adds a step.
In terms of speed: AVIVO by far. Mencoder should be faster than ffmpeg, because remuxing MP4 is much faster than splicing DVRMS. However, this may vary based on CPU and disk speed. If you can do the splice from one physical disk to another it really speeds things up. (Especially when the temp disk is a Raptor ;-) )
For ease of use: ffmpeg, no comparison.
For reliability: ffmpeg wins again. Mencoder is probably as reliable (provided the profile isn't broken!), but AVIVO definitely has some quirks.