Sprint (associates) usually can tell simply by turning off or on your phone. If you have a different ROM, they will be able to tell immediately. If you changed the boot screen, they can tell.
If you left everything the same as it was with everything stock, it'll be a bit harder to tell unless they take your phone "to the back" and open it and do some software checks. If they go into your Hboot, they can tell from there too.
By apps, they can if you downloaded apps that require root access. But at the same time, people often download apps from the Market and don't realize that the app won't work unless they are rooted so they may figure that you are a noob who doesn't know lol Such apps that require root access would include:
-Wifi tether apps (unless it's something like PDaNet or EasyTether although Sprint still frowns on any type of tethering without a tethering add-on to your plan)
-Root File Explorer
-Root CacheMate
-Overclocking apps...
Any app that requires root access will let them know whether or not your phone is rooted.
If you have added a ROM that changes the UI (user interface; the way the phone looks) some buttons may have changed and it may be learned that you aren't using the stock UI that Sprint/HTC provided such as them telling you to go to your phone dialer on an ASOP ROM and inputing a code (generally, it won't work on an ASOP ROM) or going into settings and changing something only to find that that feature was removed in the ROM or that feature is not working in that ROM.
Over the phone is harder to tell whether or not someone is rooted. If she/he asks you "are you rooted", it's best to say no. If they ask you about an app that requires root access, tell them that you tried using the app, but it doesn't seem to work on your phone...basically act clueless about anything root related lol
and on a need-to-know basis.