Most of it has been said, so here's what I'd add to the good points of others:

1. As part of the assessment (on which you make notes), hang out at each house (not in it, but around it) and say hi to a neighbour who comes out, chat about the "nice, quiet, friendly street" and see what sort of reaction you get.  I once went to view a house that interested me, and the owners only wanted to show on Sundays. House was bought and then I learned that the gas station on the corner had a bell clanging every time a car pulled in for gas...closed on Sundays. 

2. Google the street, and see if newsworthy items appear in the first 2-3 pages.  (Of course, it doesn't promise anything either way, but there may be value in having knowledge of the past.)

3. Pretend you (new homeowner) are seriously going to paint every inch of the house personally.  Walk around the home with the eyes of one doing upkeep, not buyer.  Does that change anything?  Make notes!

 4. If they did a whole list of pros and cons and one house comes out the clear winner but buyer is still acting like more investigation is needed, consider the possibility that buyer has actually chosen the house they "shouldn't" and is trying to find justification for it.

I've found that when it comes down to 2 homes, usually the energy costs and running expenses make all the difference.  People often consider can they afford to buy the home but often forget to ask can they afford to live in it!

I have them make a list of their wants/needs and the pros/cons for each - they can pretty much make up their mind half way through the list

Point out the pros and cons of both properties (according to your agency) and be sure that it is their choice (not yours). 

Pros & Cons comparison like Richie Alan Naggar said, plus operating costs, school districts, crime reports.

I'd also go back to both (back to back) and revisit both homes with no time crunch.

Tell them to imagine living in both houses and see themselves walking around, using the appliances, entertaining in back, and then what feels the best to you?

Making a list of pros & cons of the inside and then outside may help.

Lots of great responses here.  When this happens (I am dealing with it now) it generally is more an issue of price.  Both homes are equally nice and meet the needs. 

I make a T chart and we list benefits of each then compare.

Close your eyes, where can you see your coming home to?

Which home excites you when you drive up?

Which home makes you feel relaxed and at home the moment you step inside?

Which home can you see yourself living in 5, 10 years from now?

Which home makes you happier?

It is all about the emotions.

As Richie Alan Naggar stated. I find questions without seeing the results on paper will serve no purpose other than more confusion.

Yellow pad, line down the middle good verses bad. IF they don't have more than 15 items on each house, they need to investigate more carefully.

Have them view the home at different times of day - i.e. in the evening, weekend, morning - and see what impact the neighborhood may have on that property. Are children playing in the street after school? Are neighbors arguing or having a party? Are dogs barking? These could make a difference in their "quiet enjoyment" of the home.

Which home best reflects the desired lifestyle?

Even in a model match in a tract home development, there is typically some kind of differences -- why not make a list and write down what you see as the positives/negatives in each property?

Make two columns and compare.

Write down the pros and cons to each home. Narrow it and make a decision.

I don't pose questions. I tell them to go home, close their eyes and visualize where they see themselves living, which home they see themselves coming home to at the end of a long day at work or after a business trip, where they see themselves in their mind's eye celebrating a holiday. I've found that often clarifies their thinking.

It depends on the homes.  Questions about where and how they see themselves in the future are probably best.

ask what they DON'T like about each property.... the negative list says it all...

Let them sleep on it. If they still can not decide themselves, help them, writing down all cons and pros about those houses. Also, find out who is a decision maker:) 

Maria Sapio, I use Ben Franklin's method - draw a line in the center, give weight to some important factors and keep adding to get a grand total.

Whichever is a winner IS A WINNER!

All good answers above to help buyer make decision but it may not be the buyer's decision that matters in the end. The seller must also accept buyer's offer. 

Here is a strategy that may help buyer decide and help you seal the deal.

"Since you like them both. You don't want either to slip away while you decide. You never know if they will accept your offer until you make an offer so lets make offers on both and see what happens.

You can always rescind one of the offers when you know for sure."

Sellers receive multiple bids and have back up offers. Why can't a buyer?

It may actually give buyer more leverage in negotiations if sellers know buyer is also bidding on and still considering another home. 

My Buyers rate each home when they are in it.  The kids even get involved.

I like the Ben Franklin close too - 

Make appointments to see both houses a second time keeping in mind two points:

1. Other buyers might make offer while they are debating back & forth
2. Perhaps neither property is the perfect house for them, otherwise they might not be in a contrary about their decision

What can you ask them that will make them understand that while they are mulling, there might be other buyers putting offers together.  Unless both houses are ugly and smell like cats, they could both fly off the shelf!

Ask how they'd feel if this happened.  

I might go thru again what the couple said was important to them. Then the Ben Franklin method - they both can't be equal.

 I have buyers rate their houses as they go (on a 1-10 scale).  If one of them was a 10 and the other a 9, I ask what made the one they rated as a 9 not be a 10.  That typically clears it up for them...unless they rated them both 10s!  

Then, I pull out the legal pad, draw a line down the middle and across the middle - section #1 is house #1, #2 is house #2.  If they can't decide, the one with the most pros wins! 

Like, Richie Alan Naggar I would have then make a list, Maria.  A

I would go back over their list of must haves and needs.

Mortgage Broker responding

If the properties are Condos, I would:

#1   contact the property managemant companies and send them both a Condo Cert. to get the X-rays/Blood Work of the financial condition of the buildings in advance.

#2   contact the property manager as well as the HOA board members to see what major upcoming assements are on the horizon as knowing a $20,000 to $50,000 hit could be coming in 12 months could make the difference for the buyer.

 List the pros and cons.

I have them rate a home 1 to 10, if both are 9's I take them thru the pro's and con's of each home.  I ask what was special on each of them.

A plus column and a minus colomn for both properties

I like Joe Pryor's answer.

Play the psychiatrist: "how did you feel in that home?", that is if all the practical considerations are more or less equal e.g. location, commute, price, schools, amenities, size and so on.

It's rare that two homes would be equal in someone's mind.  I'd dig deeper and see what the pros and cons are.  Traffic, distances to work, schools, etc.

Some good answers here - reading....

Read Joe Pryor's answer!

Location and resale

parked and reading...

Right now we are in that short period just befor classes start at the University and our leases all end too.

So we had too many choices for some of these people, but while they were hesitating others jumped in and eliminated those extra choices.

Same can happen when buying, "make a choice or someone else may come along and narrow it for you by buying one of these homes".

I think a list of the pros and cons, particularly in light of their needs and the benefits of what the homes offer can help. 

Make a list of seven of the top items you would like/need in a home, and see which home comes out on top.   Usually price and location are on this list.