-Gamespot reviews mentioning the presence of NFL Europe teams in Madden 2002 and 2003 .
-Gamefaqs FAQ's mentioning NFL Europe teams in Madden 2001 and 2004.
-Cheats mentioning NFL Europe teams in Madden 06.
-Frankfurt Galaxy can be unlocked in Madden NFL 96
- Wikipedia says NFL Europe teams are in Madden 07 and in Madden 08
So it looks like its pretty much all of them past 2001 until NFL Europe shut down in 2007.
Confirmed for Madden 2002:
" @gla55jAw: Update? C'mon, don't leave us hanging. ;) "
Confirmed for Madden 06:
I don't have 08 anymore and it seems the teams may change with each game that had them.