I did one extract batch where I used Pilsner malt extract, and other extract lagers, as well. I went ahead and did 90 minute boils on all of them, due to the DMS concern. They were good beers. I can't say what effect the 90 minute boil, though, since I never have done it any other way.
It was fun, though. You just have to start with a proper volume to boil off.
Longer boils will also give you more hot break, it will increase your hop utilization - but only marginally. Also some believe you get more hop utilization if you boil for awhile to generate a hot break before adding your bittering hops for their 60 minutes.
To paraphrase an expert, Jamil, here's the deal on longer boils -- in general, a longer (90 minutes or even longer) boil reduces the creation of dms in pilsner malts. However, if you cool your wort to BELOW 140 VERY QUICKLY after flameout (we're talking minutes), there is no need for a 90 minute boil. Apparently, as long as the the wort is above 140, dms is being created. When using a counterflow chiller the wort sits there quite a while (creating dms all the while) waiting to get its turn thru the chiller. He uses a counterflow with a whirlpooler and gets his wort to below 140 in 2 to 3 minutes, and therefore has gone back to 60 minute boils.
I use an immersion chiller so I boil pils 90 minutes, and when i turn the flame off and the chiller water on, I stir with the chiller to cool the wort more quickly.
Jamil uses an immersion chiller whith forced wort circulation so he doesn't have to move the chiller once in a while like I have to do. DMS creation doesn't stop at 140, but below that temp the formation of DMS is not significant anymore.
If you have an immersion chiller, you may as well try 60 min boils unless you need the time to correct volume or it better fits in your schedule. I wouldn't go above 90 min as you may end up coagulating to many proteins and your head retention may suffer.