Problems with alignment of sequences

You can also use the alignat* environment which allows for multiple align points:

Notes:

• The alignat*= environment produces as many rl pairs as specified in the first paramater and does not insert additional space that the align environment does, so you need to insert the space that is desired between the alignment points.
• The leading & is used to ensure that the first column is left aligned. Hence the need for the double && to ensure that the subsequent columns are also left aligned.

Code:

\documentclass{article}
\usepackage{amsmath}

\begin{document}
\begin{alignat*}{6}
    &a_1,\ &&b_1,\ &&c_1,\ &&d_1,\ &&e_1\ &&\text{etc.}\\
    &a_2,\ &&b_2,\ &&c_2,\ &&d_2,\ &&e_2\ &&\text{etc.}
\end{alignat*}
\end{document}

Your alignment is perhaps better obtained using a structure like array:

\documentclass{article}
\usepackage{amsmath}% http://ctan.org/pkg/amsmath
\begin{document}
\begin{align*}
  &a_1,\ &b_1,\ &c_1,\ &d_1,\ &e_1\ \text{etc.}\\
  &a_2,\ &b_2,\ &c_2,\ &d_2,\ &e_2\ \text{etc.}
\end{align*}

\[
  \begin{array}{*{6}{l@{\ }}}
    a_1, & b_1, & c_1, & d_1, & e_1 & \text{etc.} \\[\jot]
    a_2, & b_2, & c_2, & d_2, & e_2 & \text{etc.}
  \end{array}
\]
\end{document}

The array consists of 6 l@{\ } columns - left-aligned, followed by a control-space \. \\[\jot] ensures a sizeable gap between the series, similar to that of align, while \text (provided by amsmath) does some testing to maintain the font size and is therefore superior to an \mbox construct (in general). In this case, it doesn't matter though.