Upper vs Lower Case

Converting to either upper case or lower case in order to do case-insensitive comparisons is incorrect due to "interesting" features of some cultures, particularly Turkey. Instead, use a StringComparer with the appropriate options.

MSDN has some great guidelines on string handling. You might also want to check that your code passes the Turkey test.

EDIT: Note Neil's comment around ordinal case-insensitive comparisons. This whole realm is pretty murky :(

From Microsoft on MSDN:

Best Practices for Using Strings in the .NET Framework

Recommendations for String Usage

• Use the String.ToUpperInvariant method instead of the String.ToLowerInvariant method when you normalize strings for comparison.

Why? From Microsoft:

Normalize strings to uppercase

There is a small group of characters that when converted to lowercase cannot make a round trip.

What is example of such a character that cannot make a round trip?

• Start: Greek Rho Symbol (U+03f1) ϱ
• Uppercase: Capital Greek Rho (U+03a1) Ρ
• Lowercase: Small Greek Rho (U+03c1) ρ

ϱ , Ρ , ρ

.NET Fiddle

Original: ϱ
ToUpper: Ρ
ToLower: ρ

That is why, if your want to do case insensitive comparisons you convert the strings to uppercase, and not lowercase.

So if you have to choose one, choose Uppercase.