A few things from mine:

# easy way to do things per-chromosome:
# for i in $CHROM;do *your code*;done
export CHROM="$(seq 1 22) X Y MT"

alias sv='samtools view'
alias svh='samtools view -h'

#grab the header of a VCF
function vcfhead {
    head -n 1000 $1 | grep "^#"
}

#unwad tarballs
alias unwad='tar -xzvf'

#find in the current directory
alias ff='find . -name $1'

#sum a column of integers
alias sumcol='awk '\''{ SUM += $1} END { print SUM}'\'

#sum a column of floats
alias sumcolfloat='awk '\''{ SUM += $1} END { OFMT="%4.2f"; print SUM}'\'' <$i'

#convert csv to tab-delimited
alias csv2tab='sed '\''s/\,/\t/g'\'

# convert tabs to new lines
alias tab2nl='perl -pe "s/\t/\n/g"'

#git stuff
#shows a preview of what's outgoing if you do a git push
function grout {
 git fetch origin master
 gd2 $(parse_git_branch) FETCH_HEAD
}
#shows a preview of what's incoming if you do a git pull
function grin {
 git fetch origin master
 gd2 FETCH_HEAD $(parse_git_branch)
}

#show the column headers with corresponding field numbers
#I use this constantly
alias header='head -n 1 | tab2nl | cat -n'

Not to beat this to death but I find the directory-based bash history scheme indispensable. I honestly don't know how people function with global histories.

function mycd()
{
    tmpDir="$PWD"
    echo "#"`date +%s`" $USER -> $@"  >> "$HISTFILE"

    builtin cd "$@" # do actual cd                                                                        

    #if this directory is writable then write to directory-based history file
    #otherwise write history in the usual home-based history file                    
    touch "$PWD/.dir_bash_history" 2>/dev/null && export HISTFILE="$PWD/.dir_bash_history" || export HISTFILE="$HOME/.bash_history";
    echo "#"`date +%s`" $USER <- $OLDPWD" >> "$HISTFILE"
}
alias cd="mycd"
#initial shell opened                                                                                     
export HISTFILE="$PWD/.dir_bash_history"
#timestamp all history entries                                                                            
export HISTTIMEFORMAT="%h/%d - %H:%M:%S "
export HISTCONTROL=ignoredups:erasedups
export HISTSIZE=1000000
export HISTFILESIZE=1000000
shopt -s histappend ## append, no clearouts                                                               
shopt -s histverify ## edit a recalled history line before executing                                      
shopt -s histreedit ## reedit a history substitution line if it failed                                    

## Save the history after each command finishes                                                           
## (and keep any existing PROMPT_COMMAND settings)                                                        
export PROMPT_COMMAND="history -a; history -c; history -r; $PROMPT_COMMAND"

Thanks for the tips. My suggestion might be obvious, but I generally want to find something in the same set of directories, so it's a speedup for me:

Seach R scripts in a bunch of directories

alias searchR='find /place1 /place2 -name "*.R" | xargs grep '

A few of the answers from here apply: http://www.biostars.org/post/show/6660/bioinformatics-cheat-sheet/

I have a lot of little one-liners and snippets that I don't use often enough that I've bothered to alias them, though. These I have tended to save in text files in a common directory in files called awktips.txt, sedtips.txt, and I just go and grab the line of interest as needed. Perhaps I should go through the trouble to alias some of them, but I'd probably forget the alias name I gave it anyway and have to look it up.

Heng Li's bioawk linked as hawk ;-) and virtualenv activation.

I do add lots of short term aliases when working with a specific tool as well.

Just to add two more:

Get number of sequences in a (gzipped) fasta file:

alias fasta_num_seq='zgrep -c "^>"'

Get the number of reads from a (gzipped) fastq file (note: in theory '+' could also happen as first character in the quality line):

alias fastq_num_seq='zgrep -c "^+"'