Examples

rename all .csv files into .txt files
rename .csv .txt *.csv

change all sampleID.fasta into sampleID.fna

rename .fasta .fna  *.fasta

add species name (e.g., E.coli) to all .bam files
change all sampleID.bam files into sampleID_ecoli.bam
rename .bam _ecoli.bam  *.bam

Ubuntu

error: syntax error at (user-supplied code), near "."
getting these errors, means you have another rename command (Ubuntu) which uses Perl regular expressions:

Ubuntu: rename all .csv files into .txt files (same as above, but using the "Perl" based rename)
rename 's/\.csv$/.txt/' *.csv

general: renaming a string at any position in filename (Example: change all 'dataNew' into 'data2015')
rename 's/dataNew/data2015/' *.csv

Add prefix

change prefix of all textfiles
rename 's/^oldPrefix/newPrefic/' *.txt (Perl based rename version - Ubuntu)

add project name to all .bam files

change all sampleID.bam files into projectABC_sampleID.bam

rename 's/^/projectABC_/' *.bam  (Perl based rename version - Ubuntu)

if it does not work (non-Perl rename command),  use a shell loop:
for f in *.bam ; do mv "$f" "projectABC_$f" ; done

Add file extension to set of file

# add suffix ".txt" to all files in a folder
for FILE in *; do mv ${FILE} ${FILE}.txt; done