Okay, so I am playing a lot of songs with the following tuning (low to high string): C#,G#,C#,F#,A#,D#

I am tired of tuning back to standard E when I want to practice scales, etc. What are some scales I can play in this tuning?

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just play the same scales you would in Drop D (compensate for the top string) but if you want to play along to songs in standard tuning, but raise them all by a half step if you want to play them in key with a song or something
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Scales are scales...they're just notes, they don't change when you re-tune your guitar. Obviously where those notes are will change depending on how you retune but that's really something you want to be learning before you start mucking around with your tuning.

Basically, learn some theory. Learn the notes on the fretboard, learn about intervals, learn what a scale actually is...the Crusade articles in the columns section are a good place to start. Learn how the guitar works musically before complicating matters further.
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Imagine you're in Drop D, and move everything up 1 fret.

It might be easier for you to think of it as: Db, Ab, Db ,Gb ,Bb ,Eb
That way you can see all the notes are as in Drop D only down 1/2 a step.
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