Consistency is the primary goal. So the first task is to know what "special numbers" we need and define commands for them:
\newcommand{\euler}{e}
\newcommand{\ramuno}{i}
(ramuno was how some Italian mathematicians of the 16th century called the quantity that squared gives –1; then Euler started using i).
The mathematical typography tradition usually didn't have a special treatment of these symbols. See, for example, n. 359 in Gauss's Disquisitiones Arithmeticae, where the equivalent of
$\cos\frac{\lambda kP}{e} + i\sin\frac{\lambda kP}{e}$
is found (the edition I consulted is from the Werke by the Königlichen Gesellschaft der Wissenschaften in Göttingen, vol. 1, 1863, page 450). There's no doubt what this i is denoting.

http://gdz.sub.uni-goettingen.de/dms/load/img/?PPN=PPN235993352&IDDOC=137206
However, in recent times, under the influence of physics and applied mathematics, people started to denote "constants" with upright letters. There's even an ISO regulation about this, which is compulsory in some fields where uniformity among papers and books is very important.
In pure mathematics there's essentially no rule. Do as you like or how your field is used to. Using special names for the special numbers allow you to change the appearance of your document just by changing the definition.
If you feel that there may be confusion between the "imaginary unit" (no worse name could be chosen for it) and an index (for summations, for instance), you have three strategies:
use a special denotation for the imaginary unit;
don't use i as an index;
forget about it and let the reader know from the context.
Strategy 2 is used by Graham, Knuth and Patashnik in their "Concrete Mathematics". Strategy 3 is very common in math textbooks.
\newcommand{\complex}{\mathbbm{i}}. There should be no need for\ensuremath, since you'll most likely use these "mathematical elements" inside math mode anyway/mostly. – Werner May 31 '12 at 22:45\newcommand*{\I}{\imath}and upright for e:\newcommand*{\E}{\mathrm{e}}? – Peter Grill May 31 '12 at 22:59symbolslists (on p. 68) several fonts that provide lowercase blackboard bold. (The future of course belongs tounicode-mathand OpenType Math fonts.) – Caramdir May 31 '12 at 23:02\pi– Peter Grill May 31 '12 at 23:04A_{kl}. It's about getting the message across not to comply with standards. – percusse Jun 01 '12 at 00:14unicode-mathwhich means that you can typeeandias usual and get them rendered in the "special" format. This actually helps ensure that you don't use these letters for more than one thing in your document. – Andrew Stacey Jun 01 '12 at 07:57