LaTeX tricks

The indices are not on the same height in my Hamiltonian

The dagger needs some vertical space. Use \phantom to add an invisible dagger also to the annihilation operator:
c_j^\dagger c_j^{\phantom\dagger} etc.

The standard TeX fonts are boring and look a bit thin on printouts

You are not alone. However, good alternatives to the TeX standard "computer modern" fonts are unfortunately rare. A simple and readable alternative is '\usepackage{txfonts}' in the preamble, which gives you the more robust Times Roman with corresponding math, but Times also looks very worn out. Generally, there are many very nice commercial text fonts which you can easily use with LaTeX, but finding appropriate math fonts that fit typographically is difficult (see some math examples). A large overview of what is available for free and commercially is the following math font site. If you own the licence, you can download Minion and Myriad fonts from Springer. There are some technical discussions in the Math Font Group. Check google to see whether some good solutions have come up recently.
Comments and suggestions are welcome.
Tilman Enss, 10 May 2005