Though not strictly an app, dndtools.eu is an excellent resource for 3.5 spells, feats, class and skills.
Regarding spells, you can search them using a "filter" which will allow you to search via sourcebook, class, level, school, sub-school; and much more. They have 3,900 spells on file, including 3.0 spells.
What I love about this site is they explicitly tell you exactly where to find the spell (what sourcebook and page number). This usually gets me to go and read the sourcebook, discovering new information I might not have known or considered previously.
I prefer to have a digital copy of my spellbook, and dndtools.eu makes it easy for me to copy the information into a word document and save it as a PDF. So once selected, I always have a quick reference for my spells in full detail.
Dndtools.eu only includes official WotC sourcebooks, so you don't have to worry about 3rd party or homebrew entries. The downside is Dragon Magazine isn't considered official, so nothing from there will be featured on the site.
Note: dndtools.eu does reference to items outside of the SRD. If linking to such sources is prohibited, I apologise.
I've never used it, but my brother swears by DnD Sheets. I believe you must manually enter the details for your spells. So it's useless in terms of spell searching, but good for a digital way to hold their information once you've decided on them.