mike renders to targa because After effects 6.5 and under wouldn't see the Maya native 'iff' files unless you force it by selecting 'all files' on import and checking the 'image sequence' bow.., after effects 7 can see native Maya files. Targas are huge compared to the native maya files and I see no extra quality.., targa take longer too. this is all got to do with the version mike was using, things have moved on a little since then, though having said that he probably still uses them for quality.., anyway these days you have a more of a choice.., as mentioned AVIs seem to always get a bum rap but I have never tried them. i stick with the 'iff' files.
what Im saying is if you have AE 7 (formerly referred to as 'adobesomethinginorotherincreibleexpensive) you can stick with 'iff' with no problem, and if you have below that you can force them by selecting 'all files' on import to AE from maya
may the shwartz be with you...
take it easy and life will be easy