I have a Janome 350e embroidery machine (have had it for 3+ years). The dealer sells all brands of thread, but she highly recommended that I use Madeira Polyneon. She said rayon is not as colorfast, and does not hold up as well when ironed with a hot iron. I have never had any problems with the Polyneon. I buy it from thesewphisticatedstitcher.com - the prices are the best ($2.65) and the service is amazing. If you buy 48 spools of thread, you get a free thread case.

Here's the link to the conversion chart I use: http://threadchart.info/threadchart.php?f=MADPOLY7

The MEs in my guild have all converted to Fil-Tec brand. They say it's the best and all have a different brand of machine. http://www.bobbincentral.com/embroidery.html

Bernina's seem to like Isacord threads. I'd sign up at a local Bernina dealer for their newletter & watch for sales. If the dealer has many in store events they usually offer a discount storewide. You could also do a search on line for a better price, but you also need to factor in shipping costs. As for the many colors designs require.....I have about 170 colors. I chose 3 or 4 shades from each color & when doing a design I pick one that comes close to what the design calls for. You don't have to buy every color. When using metallics slow the machine way down, use a thread net & a metallic needle.

Try the metro embroidery thread. I find it comprable to Isacord and glide by filtec.

http://metroemb.com/store/

Edited to add, I should mention I don't have an embroidery machine, I use these for LA Quilting. I think if the threads could stand up to the high speeds of a LA they can definitely stand up to an embroidery machine.

I would wonder why you were told rayon is the "best", because I would say the opposite. It's a weaker thread than poly and doesn't hold up to bleaching or wear. It breaks and frays easily and it isn't a good choice for items that are worn and washed frequently.

To get started I bought a couple of thread kits. Everyone seems to have them and the variety in the kits have been great. Then when I need a specific color I buy that one. It made it much more affordable than buying per pattern.

I buy all my embroidery supplies from http://www.allstitch.net/index.cfm
I've only found one place that sells Madeira thread cheaper but the other site is so hard to navigate that I just stick to All Stitch. Shipping can get a little pricy so my BFF and I combine our orders to get free shipping. I use the Poly Neon thread, I tried rayon and didn't like it. I have two Janome machines and they both like Madeira thread.
My advice is to try a spool or two of different brands and see which your machine likes.

Cari

I use Isacord. I usually have a color scheme in mind, and poly has a lot more colors, especially in shades.

All the machines like it. I embroider with a Pfaff 2170, but I've put it on the PQ 1500 for quilting.

The one thing that convinced me - metallic thread. I watched a big 830 at the Bernina dealer going full speed and using OESD YMNET thread ( Bernina owns that) . It never broke and did the whole design with no hitches.

I bought that Madeira chest long ago, and didn't use 85% of the colors. I sold it.

IMachineGroup.com sells isacord at the best price I've seen.

SewTrini

In my experience, rayon is shinier/smoother than poly. I agree that it is weaker & deteriorates more quickly, though. For satin stitching, I actually really like whatever brand it is that the Viking-at-Joann shops sell on mini-cones. Loads of different colors & gave a really nice finish for my machine applique. It was easy to use. I put an Aurifil 50/2 cotton in the bobbin.