Which Reference System Format?

Don't know what the most common method is but I use "UTM" which is very similar to the "MGRS" system the military uses. I find in most cases, it is much more accurate than the others and like you, I'm more used to the Military Grid System so because it is so similar to the MGRS system, I'm more comfortable with it.
Don't know about in the US but in Canada, if you ever have to give coords to a search and rescue aircraft etc., they are likely more apt to be using UTM than lon/lat etc.

Most applications, whether it is Google Earth, Microsoft Streets & Trips, or similar programs allow the user to select a format. However it appears that GPS units employ the decimal degree format.

You need to use Decimal Degrees.

We use GCS at work because it's basically unprojected data. From the hundreds of data sets I've seen, the preference is UTM followed by the state plane coordinate system.

According to the comments, I guess we should have first asked what GPSr your using. Is for the etrex or your auto navigation system?

I mentioned UTM because I just took for granted you meant for your hiking gps (etrex.) If however, you are asking about an auto navigation system such as a nuvi, then I would agree that DD is the most common.

I am referring to my nuvi. With my etrex, I am still using MGRS because that’s what I am used to. I used to be able to eyeball an 8 digit grid off a military map but that doesn't work in the outside world, and the nuvi only offers; DMS, DM, & DD using the WGS84 system.
It looks like DD is the more simple and common of the three.

Thanks again for all of the input,

Jay

I believe internally, that's what the Nuvi's work with - the other formats are there for user display preferences only - since custom POI files for Nuvis need DD - and other units I'm familiar with can import files made using Garmin's file specifications when saved as CSV files.

...personally, I like using DDMMSS for my GPS 76CX, because I make fewer transpositional errors with the numbers. Plus a minute is a mile, sorta, and I can eyeball distances on maps I print out using that format and know what distance needs to be covered.

With the nuvi, I just care about turn by turn directions, and so anything works. But, I still make some transpositional errors with the DD system for it, which can make life more frustrating.

GC

I did that when I created a POI for one of my trips south. Ended up 30 kilometers directly north of where I wanted to go. And found out the meaning of "You can't get there from here!"