Is there an alternative for Scrivener (a tool for writers to arrange ideas?)?
Celtx
Celtx is the world's first all-in-one media pre-production system. It replaces 'paper & binder' pre-production with a digital approach that's more complete, simpler to work with, and easier to share.
Kabikaboo (Click To Install)
Kabikaboo is meant to help you plan a novel, but could be used for anything that would benefit from tree-based text organization. Kabikaboo is not meant to create a formatted document - you should use AbiWord/OpenOffice/LaTeX or some other editor for that purpose.
Storybook
Storybook is a free (open source) novel-writing tool for creative writers, novelists and authors which will help you to keep an overview of multiple plot-lines while writing books, novels or other written works.
Scrivener for Linux is actually an option. The Linux version is now approaching release status.
The Beta program can be downloaded from the official forums.
The Linux version started as an unofficial offshoot of the windows port. However, it is being developed by the same developer that is working on the Windows version (which works well in WINE, incidentally), and there has been continuous work on bug-fixing and feature upgrades since it was first released. Discussion and bug reports can be found and made at the forums at Literature and Latte (the publisher).
WikidPad is another option. (Also see WikiPad's Sourceforge home.)
Some of the published writers who do the Writing Excuses podcast use Wikid Pad (for the episode where this is mentioned, see #5-34, "Story Bibles").
This part of the description caught my eye:
IDE for your thoughts
Software developers have grown accustomed to certain features from their integrated development environment that make their jobs easier. Features like auto-completion, outline views, incremental search, easy source code navigation. IDE's that provide these features can greatly increase developer productivity. wikidPad attempts to utilize some of these features to address the problem of personal information management.
For WikidPad, there is a PPA available through GetDebs. Otherwise, you can always compile it from source.
I've seen a couple people who've said they use Zim Wiki, a simpler wiki-like editor. It is available in the repos. I used it for a while, and liked it, though now I use Tomboy for quick note taking (with Ubuntu One synchronization).
Writer's Café is another possibility.
Writer's Café is a set of power tools for all fiction writers, whether experienced or just starting out. The heart of Writer's Café is StoryLines, a powerful but simple to use story development tool that dramatically accelerates the creation and structuring of your novel or screenplay
Writer's Café is commercial software, but has a limited demo version available.
You could also try Kabikaboo which is in the Ubuntu repositories. It doesn't have all of the features that Scrivener does but it is open source and may be able to help your organize what you write.