I'll second what sanjac said about diving with MDA. I've been living/diving here on Guam for about two years, and have really enjoyed all the times I've gone out with them (but have also enjoyed going out w/ GTDS). Most of the places they'll go are pretty easy and interesting, but a few really require more skill and experience (like Cocos or Ritidian) and they won't take the usual tourists there.
The daily boat locations really vary based on who is on the boat and what the weather is doing. Because they embark at
Cabaras Marina inside
Apra Harbor, it's a longer boat ride to some of the nice sites like
Nathan's Dent (but it's still a tiny island, so nothing is all that far). It's less likely you'd go up to the farther north sites like Two Lovers Wall or
Double Reef The harbor sites are pretty common daily boat sites because they're protected from the weather when it's rough outside, most are relatively shallow (usually 40-50 ft where the interesting stuff is, max ~90-120 ft for most), and they're pretty consistently at least decent. A lot of 2-tank trips will do a deeper dive outside, then stop in at one of the shallower harbor sites (like Seabee junkyard) for a second, easy dive.
The daily boats (the 8:30am M-F trips) are generally full of tourists, mostly Japanese, plus occasional US military. These tend not to be advanced dive trips, so you'll probably do fine and have a great time anywhere they'll go (coral and pretty fish are very popular). If you want to read up on likely sites for the daily boats, check out some of the harbor sites like
Gab Gab, Seabee Junkyard, the
Tokai Maru/
Cormoran, Western Shoals, and
American Tanker. Some of the closer, easy sites outside the harbor include Barracuda Rock (super easy dive; big rock+water+fish),
Hap's Reef,
Amtrak.
Blue Hole is pretty close to the harbor but can be a challenging, weather-dependent dive, so you may or may not get to it on a daily boat.
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If you want to save mad $$$ diving with MDA, buy a 5-star card for $75 (or $65 or whatever it's at right now). That gets you 6 single-tank boat rides or 3 two-tank rides (you're still on the hook for air, $6/tank delivered) and a discount on all other boat trips/purchases with them (and at a bunch of other local merchants/restaurants). There are also free, guided shore dives organized on the weekends that meet at MDA (8:30AM & 1PM, Sat/Sun) and at GTDS as well (but I've never gone out with them). They are a great way to see some interesting sites and meet fun diver people. Hit some of us up here on SB before coming out, especially if you're looking for dive buddies/ideas of stuff to do. If you want more/different diving than the boats offer, there are lots of folks here who are up for a shore dive any time. There are some great shore dives that are easy entry/exit with lots to see (Amtrak, Piti Bomb Holes/Fisheye like sanjac mentioned, Gun Beach, Tanguisson Beach).
One last note:
UnderWater World Guam (the aquarium out here) does a Dive With the Sharks thing that can be pretty neat (full disclosure: I used to work there, diving with that program). You get to dive in their 800,000 gallon main tank with all the sharks/turtles/rays and such, and touch some of the zebra sharks (with guides, of course). They provide all the gear and such. Visibility is always great, with lots of critters.
