Some things I have noticed. No particular order.

Importing.

Bug with 0 prefixed zip codes. It truncates the zero on import.  Causes corrupt data. Problem is - we never noticed it at first.

Views.

Need the ability to stop users creating views and/or changing them and/or deleting them. Day 2 - we have 24 views created by rank and file people.  Obviously no naming convention was used - and it cluttered up everyones general views. 

On views. eg. my accounts.  You cannot restrict to my accounts and say some criteria.  I dont mean hard coding the account owner in the view.  Coz otherwise we would have to create a view for each user manually and that is not practical.  sort of account owner=${user.email} or something. seems you cannot do this.

Email templates.

You have to use a from user email address.  You cannot simply use a generic email.  So, for example, if I create an alert and then notify someone I have to select me - versus our generic email address such as notify@skyytek.com 

Email Integration.

Many issues with this.  posted on other threads. Cannot deploy.

Cases.

Cannot email or attach notes to a case. 

Cannot email a response from the case by just typing in the description and hitting send. 

No concept of case history.

Web to case. No where to put company name in it seems as well as contact. we have cases that could pertain to a new customer versus one that is already there.

Mass update.

seems you can do only 100 at a time. Need to be able to do a lot more. Preferably with logic in it. eg. update my zip codes that drop the zero to put a zero in front.

New fields.

Need new records too. for many biz reasons. eg. time tracking stuff etc. warranties. 

User email addresses.

Need to be able to access more than one zoho account with the same email id. we will be having many instances of zoho as we roll it out across many companies.

Emailing contacts.

Need to be able to send email to more than one contact in a particular account. right now it seems you can only send to a particular contact and have to manually type a cc in.  also need to email to other contacts outside the account eg. employees.

User Profile.

Need job title for signature display. eg ${user.title}

Price books and quotes.

Need the quote to default to a particular price book - normally our MSRP pricing. right now you have to select the price book for each line item.

Also - price book very clunky to maintain if you have many price books and many items for sale.

Lead conversion.

when converting to an account - would be handy if you set the required fields for contact (in my case title, first name and last name) and also for potentials.  eg. some custom fields I have.

Tasking.

Task more than one person with the same task.

Calendar.

doesnt seem to tell you if someone is already booked for that time ?

seems you cannot create an event for more than one contact or set of contacts.

Quotes

seems you cannot change the default line for product details. ie. include custom fields etc and calculated fields.

Audit trail.

should be able to see that in the pro edition versus just the enterprise.

Create new tabs and attach docs to the tab.

you should be able to do this. its useful for general sales tools any company would run.

Account/Contact view.

Need to be able to print out or display via pdf or anything - all notes details, message details, case details, opps details and everything about a account in one click - including stuff at contact level.  right now you have to dig around a bit.

Thats about it for now.  Let me know if any of these are on the horizon.