I have spent the last couple months making adjustments and switching out parts to make my Giant Escape 0 more comfortable and fun to ride. Ergon grips, platform pedals, and Brooks B17 saddle have all worked in my favor.
I have the saddle height, pitch, and set back dialed in the way I want. What I am still fussing with is handlebar height. I am presently riding with the handlebars a half inch higher than the saddle. This is measured with a carpenter's level across the seat to the top of the stem.
This set up with the handlebars a half inch higher than the saddle makes for efficient peddling, good climbing, and relatively descent wind resistance.....for a hybrid at least. My problem is I get pain in the neck and upper back and sense a little too much weight on my hands with this set up. When I had the seat lower and the handlebars were 2" above the saddle I was really comfortable but the peddle stroke was not as eficient.
I would like to think with more and more riding I would get comfortable with my present setup, but I doubt it. I'm old, in pretty good condition, and switched to a performance hybrid because I could no longer deal with the discomfort of being bent over on a road bike.
So, I'm thinking I need to raise my handlebars to get comfortable. What would be the best way to do that? My Escape has a threadless headset. Also, I would be interested in hearing how others have their handlebar height set. Helpful suggestions would be appreciated.

Get a stem riser... this raises the threadless steerer height by 3 to 4". It puts your bars up at or above saddle level, ensuring a comfortable riding position. $40 but you can't put a price on comfort.

I would just get 25* or 35* angled stem and call it a day.

This is a neat tool that will show you the difference between stem length, height and angle. Getting a high angled stem like a 35-40degree won't get you much height. .5 to 1" or so for most setups.

TTBIKEFIT.COM - Stem Calculator

another tool

Stem Chart

I would go with a higher angled stem like mentioned above, and possibly a riser bar to get a little extra.

This is some great advise. Thanks. I too have been tweeking the stem height and rise on my bike. I am also considering riser bars of some sort, (maybe not apes). Possibly a stem riser? Have also thought about an adjustable stem.

Thanks for all the above comments.
A trip to my LBS yesterday and viewed the possibilities of:
.....A different angled stem
.....A hinged multiangled stem
.....A stem riser

I'm leaning toward the stem riser as it offers various possibilities and appears I could dial in just the height needed.
After finally getting my saddle height, angle, and fore and aft position set, I was shocked at how my peddling efficiency improved. So, once I get the handlebar tweeked, I'm anticipating a more comfortable ride.

I think it would depend on how much height you want to add. If it is a lot, then a stem riser makes sense. If it is a little more, than the angled stem is better--it decreases reach more than just the height increase.

A stem riser will do what adding more spacers won't do... get the bars up to where they should be. I have one on all my bikes. If that's not enough an adjustable stem to dial in the fit may be the next step. You will have a comfortable ride once you're done.

I'm thinking of doing the same on my Giant Escape 3. Been getting lower back problems as well as pain in the wrists lately, especially on long rides. Figured a riser may be worth trying.

When I asked my LBS about a riser they said the bike needs to be re-cabled. Has anyone had to do this on the Giant bikes when installing a riser?

Also curious if the OP is around, did it solve his problems or not?