So, we all have this dilemma. Hotels are expensive. Always. Like, several times more per night than my rent (even in the middle of nowhere, and I rent in the land of overpriced beachyness... or beachiness- I'm not sure of the correct grammer there). The good news is there are a few benefits to them.
1) You don't need your own shampoo. Unless you're really picky and/or allergic. I rarely use all the things they put in the room, but I find they generally replace them after day 1 because I put them in the shower (where I... use them!) instead of on the counter. So I like to take these and keep them as an emergency stash. They also work really well paired with guest towels to make your company feel plush (if you have a borderline rediculous stockpile of J&J buddies, I may have stolen and tweaked this tip from you). I also take them with me if I'm staying with friends or family (particularly the soap bars) for some occasion.
2) Rewards. Again it depends on the chain. Hilton does points + miles so you earn both, but the amount of points needed to redeem a free room can be about twice as many as their nemesis Marriott. (Disclaimer: I mostly stay at Hilton b/c my coworkers prefer it and we try to share rental cars, but I worked at a Marriott through college and I think the brands are pretty comparable). Smaller chains tend to offer less predictable rewards- for example Omni gave me a get your second weekend night free certificate awhile back when I checked in, but they don't have a specific point based program. Even online brokers are beginning to get into the deal (unlike airlines who mostly don't award miles through expedia/hotwire type purchases). However, they are usually specific to their purchase website, not the brand or all stays. I hear Radisson (part of Gold Points) has some of the best rewards, but unfortunately I really, really dislike their sleep-number beds.
Of course, there are also things to watch out for:
1) Parking. To me, this is the equivalent of a checked bag fee on airlines. Once you're there, you are stuck with it. So when you're looking around, check the prices. Especially if you are staying downtown or near a touristy area (sporting stadium, zoo, etc) where parking is premium.
2) Breakfast. This can be huge, depending on who you're traveling with. For families I think it is almost always better to stay somewhere with a free breakfast, but if that isn't possible look for rates that include it. Usually the price difference is about the amount of one adult breakfast, making your spouse and/or children nearly free. Also, even if breakfast is crazy expensive and you have no option 2.5 (see directly below), pastries from the local grocer are always cheaper than dining out.
2.5) Mini fridge or fridge. The mini is ALMOST as good as free breakfast. You can buy groceries for a fraction of what eating out costs. Mini fridges are getting relatively common at "family friendly" hotels, but always check. Full size fridges are even better, generally found in long term hotels (which do take short term reservations) which often times feature full kitchens. These hotels allow you the flexibility to make breakfast and dinner at your hotel and only eat lunch out during your daily activities, but can cost more depending on the area.
3) Internet. If you just need directions somewhere the desk staff should be able to take care of that, but if your teenagers are addicted to facebook (and the prospect of listening to them whine about it all week makes you queesy) or you need to check your work email to ensure the world didn't end (you might be an earthquake specialist in San Francisco... I don't know), this is a free bonus to look for.
4) Pools. If this is important to you, call ahead! You'll want to make sure they aren't painting the thing or doing work on it for the duration of your trip, and get an idea of the pool size, indoor or outdoor, and if there are other pools you can use (like if sister hotels are adjacent, they will usually let guests of either hotel use their pool- especially if one is indoor and the other outdoor).
5) Transportation. If you're flying in, see if the hotel offers a shuttle service that would keep you from needing a rental car or cab.