While I haven't been able to exactly recreate the sound of my Ampegs, I've been able to get fairly close using the graphic EQ on my Mesa (but the Mesa has alot more presence, especially with the current tubes I have). I should also add before hand that my preamp tubes are all JJ 12AX7s and the power tubes are Shuguang 6L6GCs...Also, I use a G&L L2500 or SB-2 (usually) through the Berg NV610.
First, I set the knob EQs mostly flat (meaning- mid at 10, bass at about 3, treble at about 2.5), but pull out both the treble and bass knobs for mid shift. Oh yeah, I always use the second channel as well, without the bright knob pulled. On the graphic, I make a wave boost pattern with the top of the wave being the 200 HZ (or 250, I can't remember exactly), with the 150 (or 100HZ) close behind and the 40 HZ a little below that. After the 200 HZ, it's pretty flat but with a slight boost on the second to last treble frequency.
Again, this is not an exact new-school Ampeg sound, which is characterized by a large bump in the 150HZ low-mid region (and a bit of a rolled-off high end)- but I consider it like an Ampeg SVT Classic+

In that it has a similar grit to the Ampeg (using the graphic EQ on the Mesa causes the preamp to overdrive at lower levels), but cuts in the mix better, is less muddy with more presence, and doesn't get so mushy at high levels without cranking it to ungodly volumes!
Also, it may be an unfair comparison as I got my NV610 (and sold my old Ampeg 810) about the same time that I got my Mesa back from the shop and subsequently sold my SVT Classic- so I actually only got to try the Ampeg through the Bergantino a half dozen times before deciding the Mesa kicked its ass! The Berg definitely has a lot to do with the sound, or rather- it accentuates what I like better about the Mesa over the Ampeg- ie -presence/ definition + headroom!
Hope that helps- it seems like alot of 400+ users like to avoid the graphic EQ (I think that it isn't tube-driven), I personally like to take advantage of whatever I have available.
Karl