Maybe a collection of things to make her day brighter? Maybe you could each do a thing and have a big collection of - 'we were thinking about how to make your day better,' stuff and if it's stuff that she'll keep using, she'll think of you and feel cared for long after a spa day or whatever (and I agree with the 'if that's not her thing she won't enjoy it' people).
Like.. think about her day, step by step.
What kind of alarm clock does she have? Does she have an ipod? There are docking ones. If not, there are ones that play CDs and you could like, secretly record your dad saying it's time to get up or something, or saying a bunch of fun things he always said to her, and put them on a CD and have it be her alarm clock - unless you think that'd be upsetting, obviously.
Does she drink coffee or tea or what in the morning? If she drinks coffee, what maker does she have? Maybe she'd like a Keurig (with a big supply of different cups, which also gives you gifts down the road) and a few travel mugs so she can take her drink on the go on the way to class or to see your dad?
Does she eat breakfast? Does she like to cook? If she doesn't but she likes breakfast, is there a place she likes in between the house and school or your dad, that she consistantly goes to (someplace she really likes, that she'll use) - like if she stops at Dunkin' Dounuts for a muffin, or IHOP for breakfast, gift certificates for there in big amounts so she can go a bunch and indulge in a nice breakfast without thinking about $.
Does she hit class in the mornings? When is she graduating? What's she planning to do after, like is she going to graduate school? Presumably she has supplies but maybe she could use a packed library copy card to defray that stupid little cost, or a gift cert. to a restaurant on or by campus.
What does she do when she's with your dad? Could they use something to do together? Does she read to him? A Kindle or a gift cert. to a local indie bookstore if she's a physical book person? Does he like books but when she's not there he has nothing, so get him an ipod with books on tape loaded up and an itunes gift cert and speakers?
Does she sit there? Does she like crosswords? Books of those? There are good books of those, from LA Times, NY Times (they even break down into levels).
Does she like to do needlework? Gift cert to yarn store? New yarn travel bag?
Does she like to go to the movies? Movie gift certificate.
What does she do for dinner? Does she like to cook? If she has cooking stuff maybe go the other way - a lot of areas have organic coops where you can order and get a big box of organic produce (whatever's in season) and meat if you like sometimes, every week or month, and you can sign up gifts for like 6 months of an organic produce box for her. The coops usually aren't expensive and you get good, interesting stuff (one here sends sheets with recipe suggestions in the boxes and stuff, it's cool).
If she doesn't like to cook, maybe a little bunch of gift certs to her favourite restaurants or takeout places, so she can choose different stuff based on mood.
What's she do at night? Sit and drink tea? Watch TV? Does she have a nice tv? Does she like old shows? There are metric tons of old shows on DVD that aren't on the air anymore - maybe you remember she used to love MASH or I Love Lucy or even Friends or whatever - you can get a giant box set...
Does she have a comfy bed? Does she like PJs? Does she like sheets and comforters? Does she like slippers? Does she take baths or showers?