vs a 60min boil a 90min boil will:
*Naturally enough - evaporate more liquid. This might result in an increase in your mash/lauter efficiency, because to get the extra liquid, you'll probably sparge a bit more. Maybe a good thing, maybe not
*Darken your wort - not a lot, but noticeably. Perhaps a bad thing if you are trying to make a very pale delicate lager. Flavourwise, the darkening means more melanoidins and related products, which might make your beer taste a little maltier - but with just a 30min increase, its going to be a pretty damn subtle difference.
*Allow you to extract a small amount of extra bitterness from your hops
*Get rid of more DMS. There wont be too many beers where 90mins isn't more than enough to drop DMS levels by a sufficient amount, even for no-chilling. There will be the occasional time when 60mins isn't enough.
*Cost you %50 more for gas or electricity than otherwise it would
*Cost you 30mins of your valuable time
I personally always boil for 90mins. Mainly because it gives me consistency of process. I'll sometimes "need" to boil for 90mins, so if I usually boil for 60, i the have to learn how my system works for two boil lengths.... I am lazy, so I boil for 90min every time and only have to learn once.
I also find it allows me consistency of product - I boil for 90min, but only add hops at the 60min mark. That gives me a full 30min to have taken a sample, just at the very start of the boil, cooled it, checked to see if my gravity was what I was expecting, worked out what impact any discrepancy might have, and what i might like to do about it. add water, boil for longer, add malt extract, add sugar, adjust my hopping - all before hops have gone in and removed any of my options. Plus as a bonus, the vast majority of my hot break has happened before the hops go in, which makes the utilization more consistent - its a small variable in the scale of things, but one that is largely removed by a 90min boil.
I dont think a 90min boil is "better" in and of itself - but i do find that a 90min boil allows techniques that help my brewing to be more consistent in terms of process and results - so its better for me in my brewery. YMMV.
TB