Q: Which awards are the most valuable uses of my miles?
A: The best use of miles is for the most expensive tickets. As stated previously, using 25,000 miles for an $89 ticket probably doesn't represent a good return on your investment, while redeeming the miles for a $2,000 ticket does.
There's no definitive breakpoint for this calculation, but a good rule of thumb is if a domestic ticket could be purchased for significantly less than $500, you should consider keeping the 25,000 miles and using them on another occasion. On the other hand, if there's no more expensive flight on your travel horizon, by all means use the miles for a less expensive one.
As a general rule, upgrades are good value, especially for long-haul flights where the added comfort is extra important. But be aware of any restrictions on the revenue ticket you are upgrading. In some cases you can only use miles to upgrade a full, unrestricted coach ticket (the most expensive available), which undermines the economics of the upgrade considerably. You also may be forced to pay a surcharge (anywhere between $100 and $500) to upgrade a cheaper coach ticket with miles.