I am changing out some lights and ceiling fans in our 4 year old house (we bought it new). I'm noticing that all of the junction boxes I've looked at so far (in three bedrooms and two baths) are not flush with the sheetrock. This is making it extremely difficult to put in new lights for the bathrooms. I've had to cut out the sheetrock around the junction boxes just so the hangers for the ceiling fans will fit.

My question... Is this normal? I feel like it's not since I'm having so much trouble installing the new lights.

No it is not normal, esp being an inch in deeper that the finish surface.

It does happen maybe a 1/4 or 1/2" at worst.

Sounds like the box was mounted, with 1/2" sheetrock in mind, then perhaps the carpenter added firring strip then the sheetrock.

The trades did not communicate.

Not sure what type or size boxes you have, probably 4 inch round plastic.

See page M6 of this:

http://www.arlcatalog.com/Miscellaneous/Langford_M.pdf

For a 4 in round extension.

Keep in mind, if any fixtures are ceiling fans, a standard box usually can only handle 35 pounds, and should be a fan rated box.

All ceiling boxes for fans are to be "fan rated" as TK indicated. If the boxes are not solidly mounted to a building structure, you are putting yourself in a position of the screw pulling out of the box or the box and fan falling, particularly with older plastic boxes. I would kill the power, replace the boxes with rated ones and shim them to fit flush or use a rated extender with a rated box. HD, Lowe's and electrical supply stores have a number of designs for fan support.

As well as support for fixtures a box recessed behind the sheet rock that far is in fact a fire hazard as well a code violation. That being said, if there is no issue with weight- extensions are made for most boxes, there is even a sleeve type fitting for receptacle boxes.

Good luck