A thread has been requested for links to handy sites like Memory Alpha http://memory-alpha.org/ So, here it is.
Nuetral Zone Starship Database(and a whole lot more in their links) http://www.neutralzone.de/database/indexfra.htm
DITL: Daystrom Institute Technical Library: http://www.ditl.org/ -Under the "Calculators" button has stardate conversion, and time/warp speed/distance calculators! You don't have to guess anymore! Advanced Starship Design Bureau: http://techspecs.acalltoduty.com/federation.html -Has VERY detail specs on many starships Jeff Russell's Starship Dimensions: http://www.merzo.net/ -Vessel size comparison from many different sci-fi shows Ex Astris Scientia: http://www.ex-astris-scientia.org/index.htm -Ship size charts, episode guide, etc. ...just to name a few.
http://startrekspecops.bravehost.com/muchronology.html tooting my own horn a tad, Mirror Universe timeline - canon and pocket books only.
The Enterprise Transcripts - handy if you need to reference something that was said. The Vulcan Language Dictionary - handy for Vulcan translations.
I absolutely love Trek Core for scripts, screencaps and 'other fancy stuff' to quote Peter, Paul and Mary. http://www.trekcore.com/ Warmest Wishes, Whoa Nellie Whoa Nellie's Picard/Vash Romance Fanfiction website: http://www.geocities.com/TimesSquare/Galaxy/7926/ Whoa Nellie's Sci-Fi Romance Fan Fiction Website is at: http://www.geocities.com/whoa_nellies2000
Gah, I was just about to recommend TrekCore... I found a line in the script for Insurrection that didn't end up in the film, and was able to use it to support something in my fanfic.
A few generalized links that should help improve your fiction writing in general... How to overcome writer's block... http://grammar.about.com/od/yourwriting/a/wblockquotes.htm 10 wording blunders that make you look stupid... http://blogs.techrepublic.com.com/10things/?p=194 75 words every science fiction fan should know... http://blogs.techrepublic.com.com/geekend/?p=1093 Monomyth article from Wikipedia... http://en.wikipedia.org/wiki/Monomyth Self-reference article from Wikipedia... http://en.wikipedia.org/wiki/Self-reference Trope article from Wikipedia... http://en.wikipedia.org/wiki/Trope_(literature)
Stealing Fire from the Gods : http://www.storymaking.com/thebook/ I found quite helpful when working on my first story. and a lot of stuff on storytelling/writing: http://www.howtotellagreatstory.com/articles/indexofarticles.html
I'm new to writing TOS/AOS (tho I wrote VOY stories--mainly "lower decks" crew--about a decade ago) but I've come to rely on the transcripts at chakoteya.net, to augment my Memory Alpha surfing. Mainly because sometimes you really do need to see the original context of a line. Since I'm writing primarily Pike and Number One, I also rely on scripts--both of STXI, "The Cage", and "The Menagerie". Tho when I did write VOY, I kept up a manifest of characters at Lower Decks which expanded on and continually updated, based on the original Roll call crew manifest. It was really useful for picking characters to flesh out, instead of just creating OCs. And for my Spock and Uhura stories, I've had a lot of help on the linguistics side of things from livejournal fans (I primarily hang out in the Trek writing fandom on LJ).