The question mentions using Roll20 to run the game, so I feel it's worth pointing out the tools that have become available since the question was posted.
The May 2014 update, "Data Delve" introduced community-developed character sheets for Roll20. Users can submit sheets for any system to a GitHub repository; submissions which are approved are available to all users for use with their campaigns. (Mentor-level subscribers can also create "custom" sheets without needing to wait on the approval process.) As should be expected, there is a sheet available for D&D 3.5, which includes a spell list for each character. This should remove the need to have a third-party tool for keeping track of what spells are available to you.
The presentation of the spell list might not be perfect (I have not played 3.5 on Roll20, so I can't comment on the utility of the sheet's spell list, only that it's available), but Roll20's character sheets are open-source on GitHub and anyone can submit pull requests to improve things. Or, if your GM is a Mentor, you can have custom tweaks for just your campaign.
The June 2014 update also added a (subscriber-only) feature called "Character Vault" allowing users to save snapshots of a character, which could be used as backups or for transferring characters between games. This could also potentially be used for saving partial characters for things such as spellbooks.
The character sheets from the Data Delve update do not and cannot include things like the entire SRD's spell list. However, Q1 of 2015 will include the next major update, "Update of Holding" which, among other things, will have a "Compendium" tool. The Roll20 Compendium is slated to be an in-game reference lookup, including the openly available 3.5 SRD and Pathfinder SRD. Other systems will likely require discussion between the Roll20 team and the game's publisher, but 3.5 is the game that matters for this question, and the contents of its SRD are definitely targeted for availability early next year.
As an unreleased feature, fine details of the Roll20 Compendium are forthcoming. However, it has been announced as something that will definitely be included in the next major update. Currently, all signs point to the Roll20 Compendium removing the need to look up information from an external source (assuming the game system in question is included in the Compendium).
From the announcement post:
The Roll20 Compendium
Nothing slows your game down more than a rules lookup. The Roll20 App will feature full support for our new Roll20 Compendium, a community-curated repository of information on the basics (such as spell definitions, stat blocks for the bestiary, class information, and more) of many game systems. Our intent is not to replace needing rule books, but rather to provide a complement to them; so when you see the “Fireball” spell on your Character Sheet and you can’t remember what the range is, a quick tap can tell you that information so you can get on with your game.
We’ll be starting with OGL-licensed information such as the Pathfinder SRD and 3.5 SRD, then working with publishers to expand this repository of helpful information in the future.
We’ll be unveiling more about this exciting new feature in a future blog post.