The later versions of 'squarenose' (i.e. facelifted) Multiplas have the Multijet diesel engine. I assume that you're looking for a diesel one? The Multijet has slightly more power - 120hp - is supposedly more efficient and I think has lower emissions, but best to check that elsewhere. The Multijet/DPF set up came in around 2006, so the earliest squarenoses have more in common with the roundnose (115 JTD).
It's the DPF in that lot that's the cause for concern. Best avoided IMHO......
As for the rest of it, there's little to choose between them. Suspension, chassis, brakes all continued virtually unaltered throughout the life of the car with the exception of a brief foray into rear disc brakes (best avoided) around 2002-3. Bear in mind that even the newest Multi will be 4+ years old now, so the condition of any car will be down to how well it's been maintained as much as it's age. The towelling-type seat fabrics on the earlier cars - up to late 2003 - don't wear as well as the later 'crazy paving' type fabric. Some squarenoses had optional leather interiors but they're rare beasts.
Have a read of this little lot for other peoples opinions:
http://www.parkers.co.uk/cars/reviews/owners-reviews/fiat/multipla/estate-2000/
Edit: Emission figures from the Parkers website are a bit weird:
170g/km for the earlier 115 JTD (same in either body shape) = Band H road tax
173g/km for the 120hp Multijet between 1 Feb 2006 and 1st Sept 2008 = Band H road tax
164g/km for the 120hp Multijet from 1st Sept 2008 - 1st Sept 2010 = Band G road tax